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Thesis

Reference

New insights into the diversity of deep-sea benthic foraminifera

LECROQ, Béatrice

Abstract

Les foraminifères benthiques sont une composante majeure des fonds océaniques. Leur importance dans le cycle du carbone est largement reconnue et ils sont couramment utilisés en paléocéanographie en tant que marqueurs des changements climatiques. Cependant, nos connaissances croissantes à leur sujet nous dévoilent peu à peu que ce vaste phylum retient encore quelques secrets, notamment quant à sa diversité et à la distribution géographique de ses espèces. Dans cette thèse sont décrits deux nouveaux genres de foraminifères agglutinés : Capsammina patelliformis et Shinkaiya lindsayi. Leur morphologies, spectaculairement différentes, illustrent parfaitement l'étendue de la richesse des foraminifères monothalames. Comme d'autres xenophyophores, S. lindsayi présente un réseau interne de conglomérats digestifs (stercomata) mais se distingue aussi par l'absence de cristaux de barite dans son cytoplasme. Des analyses élémentaires ont révélé que ce foraminifère géant (8 cm de diamètre) concentrait de grandes quantités de métaux, dont l'uranium, à l'intérieur de ses stercomata, contribuant ainsi [...]

LECROQ, Béatrice. New insights into the diversity of deep-sea benthic foraminifera. Thèse de doctorat : Univ. Genève, 2009, no. Sc. 4106

URN : urn:nbn:ch:unige-39568

DOI : 10.13097/archive-ouverte/unige:3956

Available at:

http://archive-ouverte.unige.ch/unige:3956

Disclaimer: layout of this document may differ from the published version.

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UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Département de Zoologie et Biologie Animale Professeur Jan PAWLOWSKI

New Insights Into The Diversity Of Deep-sea Benthic Foraminifera

THÈSE

présentée à la Faculté des Sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention biologie

par

Béatrice Lecroq

de

Roquebrune Cap Martin (France)

Thèse N °°°° 4106 Lausanne

Reprographie de l’ EPFL

2009

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Je dédie cette thèse à l’église de Ruminghem qui a prié une nuit entière pour

moi lors de mes difficiles premiers jours…

et surtout, à celui qui leur a répondu.

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First of all, I would like to thank all the members of my thesis jury:

Dr Tomas Cedhagen, Dr Andrew John Gooday,

Dr Hiroshi Kitazato, and Dr Purificación López-García.

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Remerciements

J’ai le sentiment d’avoir été extrêmement privilégiée tout au long de ma vie, en ne faisant rien pour le mériter réellement. Sans que cela ne puisse jamais compenser tout ce qui m’a été donné, j’aimerais dire merci, plusieurs fois merci, aux personnes qui m’ont aidée ou encouragée…

A Jan, pour m’avoir fait confiance.

A Jackie (chan), la meilleure de tout l’étage (pas sûre que tu me revoies près de la frontière alors n’oublies pas que tu restes quand même dans mon cœur). Aux gars de l’autre coté du couloir : Fabien, Loic et Thierry qui a pseudopodé ma life (on aurait quand même pu sortir plus souvent ensemble, désolée, c’est un peu ma faute…). A José, pour ses grandes qualités et pour tout ce qu’il m’a transmis. Aux petits nouveaux : Cyril, Michael (courage, merci pour votre gentillesse, et bonne chance, Cyril, pour le dessin). Aux anciens : Quique (futur éleveur de crabes phosphorescents des iles Tonga), Cédric, Ben, David, Xavier, Patrick, Délia, Yurika et mon dive body préféré : Fred (salut Fred ;) ). Au vénérable Juan (merci pour tes précieuses corrections et tes questions toujours pertinentes lors des lab meetings !), à Ilham (Shokran, passes à la maison quand tu viendras voir Rime), Slim (merci pour tes encouragements qui m’ont énormément touchée, j’espère que l’on se reverra), Raphael, Aurélia, Anouchka, et la douce Yamila. Au professeur Bény qui aime tant les petits poulpes à la niçoise, M. Wuest. A Jacqueline, Roland, Frank et André. A Wanda, Yvan, Anne, Lisbeth, Virginie (la furieuse pilote de rallye des champs) et Kevin. Au Dr Peck et à Benjamin (merci pour ton éternel sourire qui réchauffe le cœur). A Tomohiko qui fait glisser ses claquettes, à Patrick qui a tort (et que je vais humilier bientôt au Poker), à Julien, la belle Chen-Da et Luca (c’est bête que l’on ne soit devenus amis que maintenant !). A Wojciech. A Giovanni (spetacollo !).

A toutes les bonnes rencontres de missions ou de meetings. De ORI, Arctowski, Ferraz (spécialement à Janaina), Polarstern, Hakuho Maru, Tansei Maru, Håkon Mosby, Téthys II. A Pedro. Aux grands Thierry et Pierre (un jour je vivrai à Marseille et je mangerai des trucs bons, comme vous ...). A Juljiana, Edu, Asma, Raphaella, Ludwig (j’espère que tu es en train de chauffer les pistes à Thonon). A Antoine, Charly (le nain) et Blujita.

A toute l’équipe du Lausanne Water Polo (un de plus !!!).

A mes amis que je garderai toute ma vie ! Caro-ling-ling-Bambou (!!! love you baby !!!), Tao (le saaaage, le jazz man, le lionceau, mon ami…), Pop’eye (prête pour la course j’espère), la Cantunette des bois (ah, qu’est ce que je vais faire sans toi ?), A Carl (Bombyx des), Lanou et son petit Gabriel (merci de m’être restée fidèle), Alex Pardo (la manatee), Mu (la fée végétale, acidulée et pétillante), Scully (revival), Mulder, Pablo et Salvia (« you know my friends, if you have some neurones….. »), Daphné (mon inséparable sœur ennemie), Jose et Catherine, Chloé, Patricia, Sandra, Gwen, Manon-lolola (courage), Rudy et Mariana, Sarah, Maria et Montse. A Yuuka. A Miško et Nena. A Nina, reine des fleurs.

A ma famille: papa (j’espère que tu es fier de moi), ma petite maman chérie, ma sœur l’endive, Lilou, anounette (je t’aime). A Pépé et mémé (mon refuge), Jean Luc et maintenant aussi…………ZIGI, Gabibone et Gordana.

Au Baron de Münchausen, à Kuro et Shiro A Davor (ti i ja)

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Résumé

Les foraminifères benthiques sont une composante majeure des fonds océaniques.

Leur importance dans le cycle du carbone est largement reconnue et ils sont couramment utilisés en paléocéanographie en tant que marqueurs des changements climatiques.

Cependant, nos connaissances croissantes à leur sujet nous dévoilent peu à peu que ce vaste phylum retient encore quelques secrets, notamment quant à sa diversité et à la distribution géographique de ses espèces.

Dans cette thèse sont décrits deux nouveaux genres de foraminifères agglutinés : Capsammina patelliformis et Shinkaiya lindsayi. Leur morphologies, spectaculairement différentes, illustrent parfaitement l’étendue de la richesse des foraminifères monothalames.

Comme d’autres xenophyophores, S. lindsayi présente un réseau interne de conglomérats digestifs (stercomata) mais se distingue aussi par l’absence de cristaux de barite dans son cytoplasme. Des analyses élémentaires ont révélé que ce foraminifère géant (8 cm de diamètre) concentrait de grandes quantités de métaux, dont l’uranium, à l’intérieur de ses stercomata, contribuant ainsi à modifier la composition chimique du sédiment.

En recherchant l’origine moléculaire des komokiacés Septuma ocotillo et Normanina conferta, nous avons révélé involontairement une importante faune eucaryotique associée à leurs tests branchus. Cette étude a mis en évidence une richesse dissimulée à l’intérieur des tests de foraminifères ou dans le sédiment. Il semble plausible que des foraminifères nus ou de petite taille soient particulièrement difficile à observer au microscope, échappant ainsi aux études passées. Pour cette raison, afin d’améliorer notre connaissance de ce phylum, nous avons également appliqué les dernières techniques moléculaires de séquençage massif à des extractions globales d’ADN provenant d’échantillons environnementaux. Dans cette optique, nous avons parcouru les régions variables du « SSU rDNA » de différents foraminifères à la recherche du meilleur « code barre » potentiel. L’hélice 37 (région I), ayant présenté une excellente résolution aux plus bas niveaux taxonomiques, a été choisie pour tester cette approche. Nous avons donc séquencé massivement quatre échantillons de sédiment dont l’ADN global a été amplifié sélectivement pour les foraminières. Un fragment extrêmement court de cette région (36 pb) a été analysé par le séquenceur Solexa nous permettant d’identifier un grand nombre de phylotypes avec une résolution satisfaisante. Quelques séquences sont cependant restées sans attribution car trop éloignées de tous taxa connus. Nous suspectons que beaucoup de ces phylotypes sont en faite encore inconnus de la science, et que la diversité des foraminifères, en particulier celle des monothalames, est grandement sous estimée.

Finallement, nous nous sommes intéréssés à trois espèces communes de foraminifères calcaires ayant une distribution particulièrement étendue : Epistominella exigua, Oridorsalis umbonatus et Cibicides wuellerstorfi. Nos analyses phylogénétiques basées sur le SSU partiel et l’ITS de ces espèces révélèrent un flux de gènes entre les populations des deux régions polaires. Cette étude a été généralisée dans le dernier article de cette thèse en incluant des analyses de spécimens de E. exigua provenant de l’océan pacifique. L’analyse génétique des populations de cette espèce, basée sur les séquences de l’ITS montre effectivement une homogénéité globale, confirmant qu’au moins un foraminifère benthique d’océan profond pourrait avoir une dispersion mondiale. De plus, l’analyse phylogénétique d’espèces sœurs d’E. exigua indique que la crypticité de ce genre décroîtrait avec la profondeur.

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Abstract

Benthic foraminifera are major components of the deep-sea bottoms and especially of the abyssal plains. Because of their value as paleoceanographic proxies and their importance in the carbon cycle, they have been extensively studied. However, as our knowledge on foraminifera progresses, it becomes clear that this vast phylum still hides numerous secrets notably concerning its diversity and the geographic distribution of its species.

In the first part of this thesis we present two genera of agglutinated, monothalamous (single-chambered) deep-sea foraminifera new to science: Capsammina patelliformis and Shinkaiya lindsayi. Their respective morphologies are spectacularly different and reflect well the broad richness of monothalamous taxa. Like other xenophyophores, S. lindsayi presents internal strings full of digestive pellets (stercomata) but its cytoplasm displays the singularity to be deprived of barite crystals. Elemental analyses revealed that this giant foraminiferan (8 cm in diameter) concentrates high quantities of metals, including uranium, in its stercomata and thus contributes to modify the chemical composition of the sediment.

By searching the molecular origin of the komokiaceans Septuma ocotillo and Normanina conferta, we revealed an important eukaryotic fauna associated with their branching tests. This study emphasizes the significant species richness concealed in foraminiferal tests or simply “hidden” within the sediment. Some small and naked foraminifera might be out of reach with traditional microscopic observations. Therefore, in order to get an enhanced view of foraminiferal richness, we proposed to apply the recent molecular technique of massive sequencing using Solexa analyser and global DNA extractions of environmental samples. For this purpose we investigated variable regions of foraminiferal SSU rDNA and identified the helix 37 (region I) as the best potential “barcode”

at lower taxonomic level. To confirm the relevance of this approach, we performed the massive sequencing of four sediments targeting foraminifera and using an extremely short rDNA fragment from region I (36 bp). We succeeded to identify quite a high number of phylotypes with a satisfying taxonomic resolution. However, some sequences remained indeterminate since they were considerably divergent from any of known taxa. We suspect therefore that several phylotypes are effectively unknown to science and that foraminiferal species richness has been largely underestimated.

Finally, we examined the distribution of three widely dispersed calcareous morphospecies: Epistominella exigua, Oridorsalis umbonatus and Cibicides wuellerstorfi.

Phylogenetic analyses of their partial SSU and ITS rDNA sequences show that gene flow occurs between Arctic and Southern Ocean populations. This study was extended in the last paper of this thesis including analyses of E. exigua specimens from the Pacific Ocean. These ITS-based analyses show that E. exigua presents a global homogeneity confirming that at least one deep-sea species could have a world-wide dispersal. Moreover, investigations on partial SSU sequences of different Epistominella sister species indicated that the crypticity of this genus would decrease with depth.

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Table of Contents

Résumé ... vii

Abstract ... ix

Table of Contents ... x

List of Figures ... xii

List of Tables...xiii

CHAPTER 1: GENERAL INTRODUCTION ... 1

1.1 Diversity: context and rational... 1

1.1.1 The unnatural concept of “species” ... 1

1.1.2 Richness and diversity... 6

1.1.3 Why study diversity?... 10

1.2 Deep-sea ecosystems patterns... 13

1.2.1 An odd and ordinary world ... 13

1.2.2 Patchiness and transience of resources: ephemeral benthic oases ... 18

1.2.3 The deep-sea benthos continuum ... 22

1.3 The foraminiferal model... 30

1.3.1 General ... 30

1.3.2 A wide benthic taxa for a wide range of niches... 33

1.3.3 The typical deep-sea citizens... 37

1.4 Objectives and impacts ... 41

CHAPTER 2: THE VAST FORAMINIFERAL DIVERSITY IS INCOMPLETELY EXPLORED: MONOTHALAMOUS EXAMPLES ... 43

2.1 Introduction ... 43

2.2 The ‘mica sandwich’; a remarkable new genus of Foraminifera (Protista, Rhizaria) from the Nazare Canyon (Portuguese margin, NE Atlantic) ... 45

Abstract... 46

Introduction ... 46

Methods... 47

Results ... 49

Concluding remarks... 60

2.3 A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis... 61

Abstract... 62

Introduction ... 62

Material and Methods... 64

Results ... 66

Discussion... 74

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CHAPTER 3: “HIDDEN” RICHNESS REVEALED BY MOLECULAR TOOLS... 79

3.1 Introduction ... 79

3.2 Molecular analyses reveal high levels of eukaryotic richness associated with enigmatic deep-sea protists (Komokiacea)... 81

Abstract... 82

Introduction ... 82

Material and Methods... 84

Results and Discussion ... 86

Conclusions ... 98

3.3 Assessment of the deep-sea foraminiferal richness by massive sequencing with Solexa analyser ... 99

Abstract... 100

Introduction ... 100

Material and Methods... 103

Results and discussion... 106

Conclusions ... 124

CHAPTER 4: COSMOPOLITANISM ...125

4.1 Introduction ... 125

4.2 Bipolar gene flow in deep-sea benthic foraminifera ... 127

Abstract... 128

Introduction ... 128

Material and Methods... 131

Discussion... 137

4.3 Global genetic homogeneity in the deep-sea foraminiferan Epistominella exigua (Rotaliida: Pseudoparrellidae) ... 141

Abstract... 142

Introduction ... 142

Material and Methods... 143

Results ... 144

Discussion... 149

CHAPTER 5: GENERAL DISCUSSION, CONCLUSIONS AND PERSPECTIVES153 5.1 General discussion... 153

5.1.1 Benthic foraminiferal richness ... 153

5.1.2 On the trail of biodiversification processes ... 155

5.2 Conclusions ... 161

5.3 Perspectives... 163

REFERENCES ...165

APPENDIXES ...189

Appendix A: Monothalamous foraminifera from Admiralty Bay... 191

Appendix B: Bowseria arctowskii gen. et sp. nov. ... 215

Appendix C: Supplementary Material of section 2.2 ... 227

Appendix D: Using 454 sequencing technology to explore eukaryotes diversity ... 229

Appendix E: Supplementary Material of section 3.2 ... 235

Appendix F: Supplementary Material of section 3.3 ... 239

Appendix G: Supplementary Material of section 4.2 ... 241

Appendix H: Supplementary Material of section 4.3 ... 243

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List of Figures and Plates

Fig. 1.1.1. Distribution of a morphological trait as a criterion for species distinction 5

Fig. 1.2.1. Models of populations dispersal and gene flow 25

Fig. 1.2.2. Diversity of microbes 28

Fig. 2.2.1. SSU phylogenetic tree of Capsammina patelliformis 58

Fig. 2.3.1. SSU rDNA of Shinkaiya lindsayi 66

Fig. 2.3.2. Shinkaiya lindsayi (binocular) 68

Fig. 2.3.3. Shinkaiya lindsayi (SEM and TEM) 71

Fig. 2.3.4. SSU phylogenetic tree of Shinkaiya lindsayi 73

Fig. 2.3.5. Elemental composition of Shinkaiya lindsayi 74

Fig. 3.2.1. SSU phylogenetic tree of Komokiacea (foraminifera) 87

Fig. 3.2.2. SSU phylogenetic tree of Komokiacea (eukaryotes: Metazoan, Fungi) 89

Fig. 3.2.3. SSU phylogenetic tree of Komokiacea (eukaryotes: Euglenozoa) 91

Fig. 3.2.4. SSU phylogenetic tree of Komokiacea (eukaryotes: stramenopiles) 92

Fig. 3.2.5. SSU phylogenetic tree of Komokiacea (eukaryotes: Cercozoa) 94

Fig. 3.2.6. Pie charts of eukaryotic richness from Komokiacea and sediment 97

Fig. 3.3.1. Map of sediment sampling, Solexa massive sequencing 104

Fig. 3.3.2. Secondary structure of SSU rDNA 107

Fig. 3.3.3. Secondary structure of foraminifera-specific expansion zone 37/f 108

Fig. 3.3.4. Taxonomic resolution of SSU rDNA variable region 117

Fig. 3.3.5. Simulated saturation curves 119

Fig. 3.3.6, Fig. 3.3.7. Phylotypes richness of SFA 2, SFA 3 122

Fig. 3.3.8, Fig. 3.3.9. Phylotypes richness of SFA 4, SFA 5 123

Fig. 3.3.10. Number of phylotypes for lageniids, rotaliids, textulariids ans monothalamous 124

Fig. 4.2.1. Sampling map (bipolar gene flow) 130

Fig. 4.2.2. SSU phylogenetic tree of E. exigua, C. wuellerstorfi and O. umbonatus 134

Fig. 4.2.3. Haplotype networks of E. exigua, C. wuellerstorfi and O. umbonatus 136

Fig. 4.3.1. SSU phylogenetic tree of Epistominella genus 145

Fig. 4.3.2. ITS divergences of E. exigua populations 147

Fig. 4.3.3. ITS sequences network (TCS) of E. exigua 148

Plate 1. Psammosphaera bowmanni 52

Plate 2. Capsammina patelliformis, (light micrographs and SEM) 53

Plate 3. Capsammina patelliformis, (SEM) 54

Plate 4. Capsammina patelliformis, (SEM) 55

Plate 5. Capsammina patelliformis, (SEM) 56

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List of Tables

Table 3.3.1. Depths, coordinates and sampling method of sediment (Solexa) 104

Table 3.3.2. SSU variable regions in literature 106

Table 3.3.3. Sequences of the six variable regions 111

Table 3.3.4. Sequences divergence between and within 14 foraminiferal morphospecies 113

Table 3.3.5. Intraspecific polymorphism in variable regions 116

Table 3.3.6. Number of phylotypes recognized by phylogenetic analyses 116

Table 3.3.7. Statistics of reads and phylotypes obtained in Solexa analyses 118

Table 4.2.1. SSU and ITS rDNA sequence data for E. exigua, C. wuellerstorfi and O. umbonatus 133

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Chapter 1 General Introduction

1.1 Diversity: context and rational

1.1.1 The unnatural concept of “species”

It would seem unwise to look into the diversity without introducing its most fundamental and universal unit: the species. Althought the “species” concept has been and is still widely used in science and numerous other fields, it appears impossible to define it in a way that applies to all organisms. And this to such an extent, that many biologists simply stopped believing in the existence of the species as a taxonomic level, i.e. category. Among them Darwin, who dedicated a great part of his work to this term but still considered it as indefinable.

« It is really laughable to see what different ideas are prominent in various naturalists' minds, when they speak of ‘species’; in some, resemblance is everything and descent of little weight

— in some, resemblance seems to go for nothing, and Creation the reigning idea — in some, sterility an unfailing test, with others it is not worth a farthing. It all comes, I believe, from trying to define the indefinable. » (Darwin, 1887).

It may be useful to start with the prior definition of the word “species”, namely its etymologic root. From Latin “speciō” meaning “see” and “speciēs” meaning “appearance”, the term “species” contains intrinsically the idea of “showing some traits”. Thus, a first definition of “species” could be “a set of organisms showing common traits specific to them”.

This definition fits to the essentialist point of view, prevailing from Aristotle to Linnaeus and describing species as “natural kinds with eternal essences”. Each and every member of a kind is sharing a common essence which is, at the same time, responsible for the traits typically associated with those members. However, this definition induces two problems. The first one is that biologists sometime failed to find traits occurring in all members of a species and the second one is that they often also failed to find traits occurring exclusively in the members of a species.

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Natural environment does not produce exact replicates but rather displays phenotypic diversity. Actually, each of the traits which constitute a species according to the essentialist definition could eventually disappear in the offspring. To conserve this definition, only the traits which will pass to the next generations (genetically inherited) should thus be considered.

Therefore, an improved definition for “species” could be “a set of organisms sharing traits which will all be transmitted to the offspring”. However, environmental parameters alone decide which traits will be, by the way of selection, transmitted. Since those parameters can not be totally predicted, one could define the species category but would fail to describe any of them.

The second problem related to the essentialist definition of species is also induced by the natural selection process. According to the definition, a trait defining a species should be unique to that species. There are numerous examples of extremely specific traits shared by asunder species. This phenomenon results from a convergent evolution creating similarities coming from independent origins (homoplasy). For instance, there are striking morphological likenesses between the shell of bivalves and that of brachiopods, however not closely related;

between the spiny stems of Euphorbiaceae and Cactaceae; between river dolphins Iniidae and Platanistidae; or even, between cuttlefish and mammalian eyes. Convergent evolutions also occur at molecular level, like for the antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cods (Chen et al., 1997) and the amino acid sequence convergence of the lysozyme from the stomach of cows and colobine monkeys (Stewart et al., 1987). In each case the same evolutionary answer is proposed to an ecological problem. At first sight, it should be a quite unlikely mechanism because phenotypic differences are supposed to be controlled by many genes. The probability that the entire set of genes implied in one phenotypic trait evolves to produce the same result than for a different and independent organism should be thus very low. However, some investigations show a totally different situation. Firstly, many quantitative traits would be actually controlled by few genes, increasing the probability of a convergent evolution (Tanksley, 1993). Secondly, recent studies tend to show that molecular homoplasies would be in fact prevalent since driven by natural selection. By compiling the homoplastic amino acid substitutions in eukaryotic proteins, Rokas and Carroll showed they were twice as frequent than expected under neutral models of protein evolution (Rokas and Carroll, 2008). At this point, it becomes obvious that no set of traits is able to include or exclude an organism in or from a species since species themselves have great similarities but

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heterogeneous members. The essentialist definition of “species” should therefore be definitively rejected.

If a set of traits can not define a species by itself, the frequencies and the persistence of each trait over generations could. After Darwin introduced how species are changing over time (Darwin, 1859b), most of the scientists agreed that an organism belongs to a species because it is part of a lineage and not because it has a particular qualitative feature. Such a lineage could be compared to a continuous entity with a distribution of gene frequency over time and over all the members of the lineage. Considering a trait, a species would thus be

“located” around the maximum of this distribution. This implies that two closely related species will share a common boundary in term of gene frequencies regarding one trait. In the same way, a species under speciation process will change progressively from unimodal to multimodal distribution of gene frequencies. A similar approach of the species concept is given in the “Population Structure Theory” (PST) (Ereshefsky and Matthen, 2005). A species is there defined only by the similarities (or variations) of its members, i.e. its traits distributions. This assumption seems correct and more universal than the essentialist definition which failed to catch the species heterogeneity over time and between specimens.

Nevertheless it weakly defines the concept and rather only describes some of its intrinsic properties. A species is indeed constituted of organisms having, at a given time, a precise distribution of traits frequencies, but does it state on what is a species? In other words, the PST presents a species as a set of individuals having a certain distribution properties regarding a given trait. Thus, the common feature shared by all species and defining them as

“species” should be “to have members non-randomly distributed regarding certain traits”. Yet, this feature is also shared with other entities than species, notably with other taxonomic levels. Therefore, the PST fails to offer any univocal definition of the species category or efficient method to separate closely related species.

A third definition for “species” is given by Ernst Mayr: "groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups" (Mayr, 1942). At first sight, this definition seems to offer a clear distinction between species and appears to be proper to this taxonomic level. Unfortunately, it also raises more questions than it gives answers. First of all, reproductive compatibility criterion does not take into account horizontal gene transfers, which also contribute to species diversification

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and distinctness. There are increasing evidences that horizontal gene transfer occurs not only within bacteria and unicellular eukaryotes (Andersson, 2009) but also within plants (Woloszynska et al., 2004), mollusks (Rumpho et al., 2008) and crustaceans (Williamson, 2003). Many biologists assume that two populations with sufficiently different traits (acquired for instance during horizontal gene transfer) should be considered as two distinct species even if they still can interbreed. This remark is especially relevant in microbiology where the interspecies boundary is hazy and horizontal gene transfer common. To resolve such conflict some kind of arbitrary limits have been established depending on the taxonomic groups. For instance, populations of bacteria or archaea having more than 1.3 % differences in the 16S ribosomal RNA gene, are currently considered as distinct species (Stackebrandt and Ebers, 2006). The second objection to the Ernst Mayr’s definition comes from the fact that the interbreeding criterion is actually also a trait, having (like any other trait) a frequency distribution across the members of one single population. This implies that the ability of a specimen to interbreed with another specimen from another population will depend on its

“position” in this distribution. This is illustrated in Fig. 1.1.1. Considering three populations A, B and C closely related and composed of respective subpopulations: A1, A2, A3; B1, B2, B3; C1, a value could be attributed to each subpopulation according to a morphological trait.

For instance, populations of birds could be plotted according to their beak size. Specimen of population A present beaks of different size among subpopulations A1, A2 and A3, with a maximum of individuals in A1, i.e. having a beak of 3 cm length. The situation of population B is similar with three subpopulations B1, B2 and B3 presenting increasing beak sizes with a maximum of individuals in B2, i.e. having a beak of 5 cm length. Considering that the beak size is as a decisive criterion to choose mating partner. If birds of A1, A2 and A3 can potentially interbreed, as well as birds of B1, B2 and B3 without being able to interbreed between A and B, both populations should be considered as distinct species S1 and S2. If birds of C1 can interbreed with A3 and B1, those three populations should also, according to the definition, consist in a species S3. Yet it is impossible, according to the same definition, since S3 is not “reproductively isolated” from S1 and S2. This fictive example show how unclear is the interbreeding criterion in the Ernst Mayr’s definition. If it should be applied to all members of the same species, the definition becomes impractical. But if only few specimen of a population should be able to interbreed for that population to be a species, any population wide enough to include interbreeding members should be considered as species.

Once again, the species concept seems to escape from its own definition.

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Figure 1.1.1. Distribution of a morphological trait as a criterion for species distinction. A1, A2, A2, C1, B1, B2 and B3 represent birds populations and are plotted as a function of their beak size. S1, S2 and S3 represent hypothetical species according to Ernst Mayr’s definition (groups of potentially interbreeding natural populations). Barriers between S1, S2 and S3 can not be established. According to the definition, should A3 and B1 belong to the same species? In one hand, they are reproductively isolated but on the other hand, they are regrouped by C1, which can interbreed with both A3 and B1.

To conclude, it should be assumed that there is no universal definition of “species”

simply because this category does not exist in the nature. Indeed, species vary in the way they regroup organisms, do not have a common definition but rather common characteristics like a non-random distribution in the traits frequency of their members. Darwin also wrote:

“I look at the term species as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other (...) It does not essentially differ from the word variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for convenience sake." (Darwin, 1859a).

Eventhough the existence of species category (i.e. taxonomic level) has to be rejected;

there should be no doubt about the use of the species taxa (like for instance Raphus cucullatus or Epistominella exigua) as the first and foremost convenient evolutionary units, which representatives have been arbitrarily chosen and which traits evolve over space throughout their representatives and over time from their appearance to their extinction.

Species distinction according to a morphological trait

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1.1.2 Richness and diversity

The species richness is simply defined by the number of different species and can be established, for instance, inside a given area, at a certain time or within a community. The biological diversity or “biodiversity” is the "variation of life at all levels of biological organization" (Gaston K. J., 2004). It can refer to the species diversity, the genetic diversity, the ecosystem diversity, or to any other biological variety. For the moment, we will focus on the species diversity, which reflects both the species richness and the number of individuals from each species (Margurran, 1988).

Nowadays, the relevance of both richness and diversity seems obvious in any biological study linked to natural populations. However, these two concepts, as they are currently used in ecological context, are quite new. Indeed, taxonomy exists since thousands of years, whereas it is only in the second part of the 19th century that biologists headed toward ecology, probably in the background of an already declining environment. Ecology, introduced by Ernst Hackel (Haeckel, 1866) and initially developed by Eugenius Warming (Warming, 1895), examines the interactions of living organisms with their environment. The development of this new field reflected thus a slide in biologists’ concerns, from a particular to a global and contextual point of view. Actually, during this period, a real and deep upheaval was occurring, in the scientific thought as well as in the experimental methods.

Biology became less contemplative and was not restricted anymore to the description and study of natural examples. On the contrary, main issues were, from that moment, to understand the relationships between biotic units and abiotic factors with the inherent purpose of acting on the overall system and modifying it.

The first crucial step of the ecological approach, and also the one which will be mainly discussed in this thesis, consists in the assessment of the diversity. Since the work of Whittaker, tree levels are widely used to define the diversity: the Alpha, Beta and Gamma diversity. They are representing respectively the within-habitat, cross-habitat and regional diversity (Whittaker, 1972). Before assessing any richness or diversity level, an ecological purpose is required. For instance, studying the impacts of industrial activity on a natural swamp will imply investigations on alpha diversity, while comparing bacterial fauna from two different types of environment will involve the Beta diversity. There are several metric

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ways to quantify the species richness and diversity of an ecosystem. The most common involve the calculation of the Simpson Index (Simpson, 1949), which represents the probability that two randomly selected individuals in the habitat belong to the same species, or that of the Shannon Index (Shannon, 1948), which accounts for both abundance and evenness of the species and which is maximum if each species represented is composed of the same number of individuals. Nevertheless, some ecologists consider that species number is a poor unit for evaluating biodiversity and highly depends on sampling. For that reason, Warwick and Clarke have introduced the taxonomic diversity index and the taxonomic distinctness, which both take into account the phylogenetic separation between individuals (Warwick and Clarke, 1995).

No matter what method is chosen for the diversity assessment, the work always includes the specimen counting and their identification. Once again, numerous different ways exist for counting and identifying organisms depending on the characteristics of the group studied, like its body size range or its occurrence. Identification criteria truly depend on taxa even if morphology remains, until today, widely used. However, morphological studies are sometimes insufficient or excessively time consuming as identification tool. Biochemical analyses, such as fatty acids composition, are often performed for the identity diagnosis of the smallest organisms (Cox et al., 2006; El Menyawi et al., 2000; Roberts et al., 2006). Quite rapidly after the rise of the molecular systematics in the late 1960s, the genetic information contained in the DNA and RNA also became a standard for the identification. The use of this powerful molecular tool is now more and more systematic in the identification process but the investigated regions differ depending on the group, the family or even the genus studied. For instance, DNA sequences of some nuclear genes enabled the distinction between the African elephant species Loxodonta africana and L. cyclotis (Roca et al., 2001); small subunit ribosomal DNA (SSU rDNA) has been used to identify apicomplexan parasites of tortoises (Traversa et al., 2008) and microbiologists refer either to SSU or to internal transcribed spacer (ITS) rDNA to dissociate strains of bacteria (Chen et al., 2001). In 2003, Paul Hebert proposed that partial sequences of the cytochrome c oxidase subunit I gene (COI) from the mitochondrial DNA (mtDNA) would be kinds of species specific barcodes and would provide

“a new master key for identifying species” (Hebert et al., 2003). Unfortunately, there are now clear evidences that the COI gene does not suit to identify species in all taxonomic groups either because it may be represented by heterogenous copies (Song et al., 2008) or because it

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is not diverging rapidly enough (Elias et al., 2007; Huang et al., 2008). However, continuous efforts to find reliable short DNA barcodes are still produced for each taxonomic group separately and give sometimes positive results (Huse et al., 2008). Thus, DNA barcoding (if not only based on COI) offers a competitive solution for the diversity assessment and its management, since it potentially provides a fast and relatively cheap way to identify species (Rubinoff, 2006).

As for the species identification, the specimens count is performed based on direct or indirect evidences that the species is or was indeed present in the studied area. For instance, diversity of insects is usually established by in situ trapping and direct counting (Abdullah et al., 2008). For terrestrial mammals like coyotes, number of individuals is often estimated by collecting feces (Kays et al., 2008) and for bacteria, richness can be found using clone libraries of rRNA genes (Polymenakou et al., 2009). All the methods to assess the species richness and the diversity are not equally relevant and indirect evidences can sometimes be misleading. Remains and metabolites can be dragged out of their original place by the wind, the current or another organism. The best way to be sure that a species is indeed in a given area is by observing it alive directly in its ecosystem, which is of course impossible for many taxa. Moreover, some studies suggest the presence, in marine sediments, of extracellular DNA, which could be preserved for a long time after the death of the organism it comes from (Dell'Anno and Danovaro, 2005a). These “dead” DNA molecules could potentially be amplified and included in clone libraries, inducing wrong conclusions about the species richness. Finally, a particular attention should be paid to the “active part” of the diversity.

Since molecular tools are getting more and more efficient, they enable to reveal a great richness including numerous new taxa from the environmental samples. The ecological meaning of this diversity should be taken in account, since all the species recovered by molecular analysis may not be equally involved in metabolic processes of ecosystems.

After the assessment of the diversity for a given area, an ecological approach should lead to the factors that are associated with the species richness and the species occurrence in this area. Three kinds of events can modify the local species richness and thus, the diversity:

speciation, extinction and migration in and out of the studied area from and toward a regional gene pool (Gage, 2004). Thus, to identify the factors shaping the richness, it is first required to find what could generate these three events.

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An ecosystem with a set of populations from different species can only support a finite amount of biomass regarding its physicochemical characteristics like, for instance, light exposure, resources availability or nesting sites. There are two opposite ways to consider the populations occupying the ecosystem. The first one is based on the ecological niches concept (ENC) assuming that each species possesses its own characteristics, which make it suitable to occupy a particular space, so called “niche” (Grinnell, 1917). It implies that each species has a different fitness regarding the environment. After a certain time, a niche will be occupied by only one species: the one with the greatest fitness. Grinnell presents the niche as a property of the environment. According to him, the nature will supply to each new niche a new occupant, selected by evolutionary processes. However, it remains unclear whether new species are indeed produced by niches creation or whether competing species tend to use different resources to avoid competition and so, create niches. In the latter case, ecosystems should evolve by partitioning natural niches and would continuously increase their species number.

Evidently, Grinnell’s concept could be criticized for being totally devoted of randomness, since it implies that new species could only be produced by competition.

The other way to consider populations occupying an ecosystem refers to the neutral theory of Kimura, which gives a predominant place to genetic random drifts in evolution (Kimura, 1979). This will lead Hubbell to later introduce the unified neutral theory of biodiversity (UNTB), setting that all species and individuals of the same trophic level are equivalent (Hubbell, 2001). In other words, all species have “neutral” differences and similar chance of success in a given ecosystem: they have thus similar fitness. Considering a closed ecosystem and according to the UNTB, genetic drift would induce speciation at the same global frequency for each population. At the beginning of this process, population’s size could be large and obey to the same deterministic models, for instance, prey-predator interactions. When preys population increases, predator population increases too, inducing a growing consumption of preys and so on, until an equilibrium state. Balances will be successively reached between populations of smaller and smaller size, while species are drifting and speciation is occurring. As a consequence, the number of species should continuously increase with a decreasing size of their respective populations, since those sympatric species are competing for similar resources. The UNTB predicts that this process will go on and on until the populations size becomes so small that species obey to stochastic models. Random events (like fire or disease) will eliminate species as fast as others will

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appear, producing, this time, an equilibrium between species (Levinton, 1979). This vision meets somehow the theory of island biogeography, describing the colonization process of a virgin island. A steady-state of the species richness is reached when there is equilibrium between immigration and local extinction (MacArthur and Wilson, 1967). According to UNTB, any new ecosystem will evolve by continuously increasing its species richness and decreasing its species respective abundance until equilibrium, where the system is biotically saturated with individuals. Thus, at steady state and without any perturbation of the system, species richness would be predictable (maximized regarding the area size) and population densities constant. These conclusions, only valid for species competing at the same trophic level, induce that diversity per unit area would tend to be the same everywhere.

Both ENC and UNTB agree that the species richness of an undisturbed area will increase with time. Assuming that, it becomes clearer that there are no factors directly associated with the species richness and the species occurrence, but rather different evolution states from the moment when the system was disturbed. Area with low species richness would thus be young ecosystem resulting from new niches partitioning or having been recently disturbed and passed through a bottleneck. Other way round, hotspots of diversity would be old undisturbed system close to the steady state.

1.1.3 Why study diversity?

First and foremost, it has to be pointed out that very little is known about the biodiversity. Living organisms have been given names since ages, but till the end of the 17th century, only species of the same range of size as that of humans were considered. Microbial diversity, which forms the greatest part of the global diversity, remained totally unknown until microscopic observations of Leeuwenhoek. Today, between 1.5 and 2 million eukaryote species have been formally described (including redundant descriptions and considering only the world-wide accepted literature) and would constitute, according to the latest estimations, between 10 and 20 % of the entire eukaryotic richness (Gonzalez-Oreja, 2008). Prokaryotic richness is represented by less than 5000 described species, while some scientists estimate the actual number close to 4 million (Curtis et al., 2002). Other authors doubt about the accuracy of any speculation since essential parameters required by models are still unavailable (Curtis

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et al., 2006; Ward, 2002). Increasing our poor knowledge on global diversity will surely lead to a certain benefit.

A second argument to study diversity comes naturally from the value of the species themselves. Besides aestheticism and well-being that they provide to humans, species are the main actors of the global ecosystem humans belong to. Investigate the diversity pattern contributes to understand voucher systems involved in human requirements like food, air and water quality, or drugs availability. For instance, last pharmacology global report indicated that, only during 2005-2006, 183 chemicals from marine organisms have been shown to have one or several biological activities of medical interest (Mayer et al., 2009). Goods that humans need are likely to be found almost anywhere in the nature, on the condition that the global species richness remains sufficient. Since they are increasing evidences of redundancy among species metabolites (Wood et al., 2005) we should be able to find, anytime despite the species natural turnover, organisms producing a molecule of interest or fulfilling a desired function. However, it seems quite more difficult, or at least much longer, to invert a process of biodiversity loss. For that reason, it is probably more urgent to study mechanisms involved into the diversity maintaining rather than study the species themselves. This last remark might be true to such an extent that the diversity would consist in a real necessity for the human species, without which it could not perpetuate. Indeed, Homo sapiens is poorly extremophile and incredibly delicate species with extensive requirements to survive. The picturing of human as a “superior” species able to extract any kind of goods from its environment could be counterbalanced by the one of an “invalid” species, physiologically deficient, since dependant on numerous other species. A major reason why humans survived over two hundred thousand years with increasing abundance might be that they came across an environment with high diversity and, by chance or as an evolutionary issue, were able to use it extensively.

The last points concern the involvement of diversity into the productivity and the stability of ecosystems. The overall value of biodiversity may reside in how it affects ecosystem functions. Several investigations established a relationship between biodiversity loss and ecosystems functioning (Bunker and Naeem, 2006; Danovaro et al., 2008b; Fox, 2006; Loreau, 1998; Tilman, 2001). According to the functional insurance theory, diversity would protect ecosystems against declines in their functioning because high number of species will increase the chances that, at least, some of them maintain those functions if others

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fail (Diaz and Cabido, 2001). It is still debated if adding species to an ecosystem will increase its functioning continuously (so called the “rivet hypothesis”) or only up to a certain point where some of the species will start to share same functions (known as the “redundancy hypothesis”). It is also pointed out that diversity alone might not be able to provide stability to ecosystems and is only one contribution in a complex and wider global process (Ives and Carpenter, 2007; Valone and Barber, 2008). However, diversity seems to largely contribute to the stability of ecosystems and thus, to their durability (Pfisterer and Schmid, 2002;

Tylianakis et al., 2006). Numerous studies looked also for correlation between productivity and diversity since it was crucial issue from an economical point of view. Most of those researches converged to affirm that diversity, among other parameters, would not only buffer but also enhance ecosystems productivity (Witman et al., 2008; Yachi and Loreau, 1999).

To conclude, it is certain that human destiny is linked to the biodiversity of the planet.

Diversity loss, like it seems to be occurring right now in most of environments (Ling, 2008), will certainly have direct impact on ecosystems functioning and productivity. Despite all, scientists are late to study processes involved in the species richness maintenance and even fail to give estimations of diversity for many taxa. Tremendous amounts of money are worldwide spent to balance losses induced by extinction or populations reduction of target species with commercial interest, instead of being used for the study and the protection of biodiversity. At the “World Conference on Marine Biodiversity” holding in Spain during November 2008, Rudolf de Groot presented some socio-economic costs of marine biodiversity protection:

“It is calculated that effective protection of 20-30% of the world’ seas and coastal systems would cost between 5 and 19 billion US$ per year but will generate benefits many times that amount. Current global expenditures on supporting (non-sustainable) marine fisheries are estimated between 15 and 30 billion US$ per year.”

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1.2 Deep-sea ecosystems patterns

1.2.1 An odd and ordinary world

Seventy-one percent of the earth surface is covered by water accumulated by outgassing, over the past 4.6 billion years, or from extraterrestrial origin (brought with comets). Oceans represent 97.3% of this water and are, for 95%, considered as deep sea, i.e.

deeper than 200 m below the sea level. Therefore, it is correct to affirm that the deep sea is the most common environment of the planet. However, it is still regarded by many scientists as one of the most unusual and fairyland-like biotope of the world. For a long time, deep sea was even not fully considered as a biotope and many have speculated that life would not occur very deep. In the early 19th century, how deep extended oceans and living organisms was still a complete mystery. After a dredging campaign on Aegean Sea in 1841, Edward Forbes proposed the “azoic theory” based on his observations of a fauna getting rarer with depth.

According to his extrapolated curve of rarefaction, life should disappear around 550 m (Forbes, 1844). It is remarkable that this erroneous theory held for almost 25 years, despite contrary evidences (Anderson and Rice, 2006). The “recording telegraph” invention, two years later, was about to bring one of those evidences and change the history of marine biology. The installation of transatlantic telegraphic cable between Ireland and the Newfoundland revealed deep-sea bottoms of 5000 m and a living specimen of Caryophyllia borealis (a stony coral) attached to the cable at 1800 m. From that moment, marine biologists’

mind got carried away by this question alone: “How deep occurs life in the oceans?”. Still, they will have to wait more than a century to get the answer. Finally, in 1960, Jacques Piccard and Don Walsh on board submersible “Trieste II” reached the deepest known ocean point at 10’911 m disturbing, by the way, flounders and shrimps of the Mariana Trench. Today, almost fifty years later, this record is waiting to be repeated and less than 1% of the deep sea has been explored. One of the reasons why abysses were unstudied during such a long time and why they still remain more mysterious than the dark side of the moon, is probably that they drastically differ from the terrestrial environment scientists are living in. First, because this aquatic milieu has a density about 830 times that of air and a viscosity about 60 times greater, directly ruling the morphology, metabolism and behavior of its inhabitants. Then, considering an average depth of 3800 m, deep sea is largely deprived of natural light except that produced by the organisms themselves. As a major consequence, primary production can

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not be processed through photosynthesis, which induces a very low average concentration in nutrients and thus also, low concentration of organisms. High pressures, low temperatures and oxygen concentrations also participate to increase differences between terrestrial and deep marine environments. Since the late 1970’s, exceptions to those general features are known.

Vents and seeps, for instance, are forming real biological “hot-spots” at the opposite of other typical deep-sea ecosystems. They emphasize even more the singularity of this world.

Deep sea consists in a prodigious volume of water (1.3 billion km3) over a floor shaped by plate accretion and particle sedimentation. Traditionally, deep-sea pelagic volume is divided into four vertical zones: the mesopelagic (from 200 to 1000 m), the bathypelagic (from 1000 to 4000 m), the abyssopelagic (from 4000 to 6000 m) and the hadopelagic (from 6000 m to the bottom). The mesopelagic, also called “twilight” is clearly different from the other three realms. Just below the surface water forming the photic epipelagic, reduced light still penetrates but not sufficiently for photosynthesis. Biomass is getting poorer and is almost deprived of phytoplankton. It is also the place of vertical migrations for zooplankton, fishes, crustaceans and mollusks which follow the phytoplankton up through the water every night.

Physiological adaptations linked to the reduced light conditions, as tubular eyes or well- developed phototactic organs, can be observed in the species that do not participate in this migration. Bioluminescence is another feature widely spread among mesopelagic organisms and is known to be linked to varied function as communication (Rees et al., 1998), camouflage (Young and Mencher, 1980) or prey illumination (Douglas et al., 2000). Light is produced in photophores by specialized tissues or symbiotic bacteria (Shimomura et al., 1972). Temperature is getting down from over 20°C at the top of the mesopelagic zone (200 m) to around 4°C at its border with the bathyal zone (1000 m). Oxygen minimum zone (OMZ) also occurs in the same depths interval, depending on the atmospheric conditions and the local mixing of water masses. In the upper layers, close to the water-air interface, oxygen concentration is high (around 6 ml.L-1). Oxygen that is dissolved from atmosphere into the water and oxygen produced by photosynthesis exceed that consumed by respiration and by decomposition of sinking organic matter. Between 80 and 90% of these sinking particles are consumed by bacteria in the first 1000 meters. Going down from the surface to the OMZ, where oxygen concentration can reach less than 1 ml.L-1, contribution of atmosphere and photosynthesis is getting weaker. Deeper than the OMZ, organic matter degradation is weak, since there are only few particles left. There, oxygen concentration, also supported by cold

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deep waters (oxygen-rich) supply, increases again but remains lower than near the surface (up to 3 ml.L-1). Organisms living in oxygen deprived environment present metabolic adaptations that enable them to consume less oxygen (some bacteria and foraminifera use rather nitrate) or to extract it from the water with high efficiency, as the vampire squid with its haemocyanin of enhanced oxygen affinity (Seibel et al., 1999). It is not the point here to describe each and every chemico-physical mechanism occurring in the deep sea but OMZ plays indeed an important role by regulating the productivity and the ecological community structure of pelagic systems (Deutsch et al., 2007), both affecting the benthos. While the mesopelagic zone is the place of strong gradients and temporal variability, the rest of the deep sea consists in a much more homogenous environment with relatively stable parameters. Bathypelagic, abyssopelagic and hadopelagic zones are globally cold, poor in nutrient and oxygen, and totally deprived of solar light. At 1000 m, less than 10 % of the sinking organic matter from the upper layers remains, making all the food chains energy-poor and poorer with depth.

Organisms are therefore sparse and have to cope with nutrients limitation, cold temperature and hypoxic conditions. Numerous adaptations aim to increase their chance to eat and meet mating partners and to reduce energy consumption. Fishes, for instance, tend to be opportunist predator able to catch and swallow huge preys regarding their own size (Ebeling and Caillet, 1974; Hopkins and Baird, 1973). It has also been reported that copepods use extremely efficient mechano- and chemoreceptors to track female and food (Yen, 2000). Another striking example is angler fish male, which follows female’s pheromones, bits her and remains attached to her body for the rest of his life, saving energy and being exclusively devoted to the reproduction (Munk, 2000). In conclusion, the deeper part of the oceans is a diluted world where each source of energy is exploited to the uttermost and each opportunity is seized.

The benthic realm does not escape the poor energy and food resources constraints.

Even if the deep-sea bottom presents various sorts of topological features, nutrients density seems to shape almost alone the spatial distribution of organisms. The deep-sea relief starts near the coast with the continental slopes, usually in the range of 300-2000 m, and meets up the abyssal plain at 4000 m in the mean and deep trenches at the deepest points. These three major environments are actually connected with those not only above but also beneath the ground. Oceans bottoms receive unevenly organic matter from the upper water layers depending not only on the surface production and consumption but also on the ability of their

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form to retain the sediment. Upstream input consists first in marine snow accumulated especially in the bowl-shaped places (Alldredge and Silver, 1988; Lampitt, 1996), then in carcasses of larger organisms like whales or kelps (Graham et al., 2007; Lorion et al., 2009), and finally in terrestrial sediments dragged from the coast through submarine canyons (Canals et al., 2006). Consequently, the surface of most areas consists in mud and organic ooze, except for some rocky bathyal slopes and trenches. Matter input also comes from underneath the ocean floor due to geological activity of the tectonic plates. Under the mid-oceanic ridges, convection currents in the magma rise from the mantle core through the oceanic crust and emerge as lava. This induces a high volcanic activity with frequent earthquakes and faulting.

Hydrothermal vents, discovered only 30 years ago (Corliss et al., 1979), are among the features created by these events. Seawater that has permeated into the ocean floor is heated by the hot magma (up to 350-400°C) and enriched in metals (mainly iron, copper and zinc) and hydrogen sulfide by dissolution from the surrounding crust. The hot and less dense hydrothermal fluids rise up through the ocean crust before exiting the chimney and mixing with the seawater. Because the seawater is cold and oxygen-rich, it induces the precipitation of metal sulfides and oxides resulting in a black smoke which led to the nomination of “black smokers”. When the water reaches only 250-300°C, hydrothermal fluids flow more slowly than in a black smoker and thus, can mix with closely permeated sea water (cold) already under the sea floor. In this case, metal sulfides and oxides precipitate into black minerals before exiting the chimney. When the fluids finally get out in the open ocean, only silica and calcium sulfate (white) are left to precipitate, leading to the white color of the “white smokers”. A huge biomass is associated with the smokers, starting with thermophile chemosynthetic bacteria, which insure the primary production without photosynthesis by oxidizing sulfite ions from the vents into sulfur (CO2 + H2S + O2 → CH2O + H2SO4) (Kaiser, 2005; Ruby et al., 1981). This primary production enables directly or indirectly the occurrence of many other life forms each of them deeply specialized and typically associated with most of hydrothermal vents ecosystems. Some organisms graze on bacteria, while others host them in their tissues or feed on primary and secondary consumers. A famous example of endosymbiosis with the chemosynthetic bacteria from the vents is the giant gutless tube worm Riftia pachyptila, consumed by the hydrothermal crab Bythograea thermydron, which is itself hunted by both octopus Vulcanoctopus hydrothermalis and eelpout fish Thermarces cerberus (Childress and Fischer, 1992).

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Along continental margins occur other special features of the deep-sea bottom called

“cold seeps” and consisting in seepage of hydrogen sulfide, methane (sometime methane- hydrate ice) or hydrocarbonated fluids (Dugan and Flemings, 2000). These fluids are released in the form of brine and settle along the bottom like lakes, because of their high density.

Living communities associated with the cold seeps are similar in density and composition to those found near the hydrothermal vents and include, at the base of the food web, chemosynthetic bacteria metabolizing sulfides and methane (Knittel et al., 2005). Compared with the short lasting vents (a couple of years only) cold seeps are relatively stable systems sheltering among the longest living invertebrates, as the tube worm Lamellibrachia luymesi, which can live up to 250 years (Bergquist et al., 2000).

The third kind of special habitat induced by geothermal activity is also found near the continental margins and is composed of mud volcanoes and seamounts. Mud volcanoes are also considered as a kind of seep and consist in a mixture of mud, water and gases (mainly methane) forming characteristic domes at the surface of the sea floor. Immediate surroundings of mud volcanoes are found to be rich in micro-organisms and notably, there again, in chemosynthetic bacteria (Niemann et al., 2006). Seamounts consist in undersea mountains (typically extinct volcanoes progressively covered by sediment) higher than 1000 m. Because they are from volcanic rock, they offer a substrate much harder than the surrounding sedimentary floor and thus shelter different types of organisms including suspension feeders as sponges and corals. Moreover, their shapes disturb deep currents and induce upwelling, which bring nutrients to the euphotic zone. This locally enhances biological activity and increases concentration of living organisms. For that reason, seamounts are strategic stops for large migratory animals and also aggregate numerous visitors (Morato et al., 2008). Finally, the deep-sea bottom appears to be much less featureless than it has been supposed during the past. Local geological events create remarkable habitats for remarkable organisms.

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