A biogeographic network reveals evolutionary links between deep-sea hydrothermal vent and methane seep faunas

Reevaluation of the Systematic Status of Branchinotogluma (Annelida, Polynoidae), with the Establishment of Two New Species

Branchinotogluma is one of the most diverse genera among the polynoids inhabiting deep-sea chemosynthetic environments. A total of 14 species have been described from the hydrothermal vents and cold seeps worldwide. Our phylogenetic analyses based on four genes (COI, 16S, 18S, and 28S rRNA) recovered the current Branchinotogluma as paraphyletic, with seven clades scattered in two main clades. The monophyly of the main clade composed of Branchinotogluma (except Branchinotogluma segonzaci), Branchipolynoe, and Peinaleopolynoe is supported by the presence of 20–21 segments with 9–10 pairs of elytra, ventral papillae starting from segment 12 in males, and arborescent branchiae. The monophyly of another main clade composed of B. segonzaci, Bathykurila, Lepidonotopodium, Levensteiniella, and Thermopolynoe is supported by the presence of usually 22–30 segments with 11 pairs of elytra and the lack of ventral papillae in females. In addition, our study recognized two new species, Branchinotogluma nanhaiensis sp. nov. and B. robusta sp. nov., based on specimens collected from the deep-sea cold seeps in the South China Sea. Both the morphology and molecular phylogenetic analyses support the validity of the two new species and the sister relationships between B. nanhaiensis and B. japonicus and between B. robusta and B. pettiboneae as well.

Species assemblage networks identify regional connectivity pathways among hydrothermal vents in the Northwest Pacific

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore the structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are "oases" of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of species assemblage networks at hydrothermal vents, how local and regional parameters affect their structure, and the implications for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity and a bipartite network of species nodes linked to vent site nodes at which they are present. Using these networks, we assessed the role of individual vent sites in maintaining network connectivity and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonization routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multivent impacts from proposed deep-sea mining.

Does substrate matter in the deep sea? A comparison of bone, wood, and carbonate rock colonizers

Continental margins host methane seeps, animal falls and wood falls, with chemosynthetic communities that may share or exchange species. The goal of this study was to examine the existence and nature of linkages among chemosynthesis-based ecosystems by deploying organic fall mimics (bone and wood) alongside defaunated carbonate rocks within high and lesser levels of seepage activity for 7.4 years. We compared community composition, density, and trophic structure of invertebrates on these hard substrates at active methane seepage and transition (less seepage) sites at Mound 12 at ~1,000 m depth, a methane seep off the Pacific coast of Costa Rica. At transition sites, the community composition on wood and bone was characteristic of natural wood- and whale-fall community composition, which rely on decay of the organic substrates. However, at active sites, seepage activity modified the relationship between fauna and substrate, seepage activity had a stronger effect in defining and homogenizing these communities and they depend less on organic decay. In contrast to community structure, macrofaunal trophic niche overlap between substrates, based on standard ellipse areas, was greater at transition sites than at active sites, except between rock and wood. Our observations suggest that whale- and wood-fall substrates can function as stepping stones for seep fauna even at later successional stages, providing hard substrate for attachment and chemosynthetic food.

Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences

Precise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.

Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities

The topography and hydrography around seamounts have a strong influence on plankton biogeography. The intrinsic properties of various biological taxa inherently also shape their distribution. Therefore, it is hypothesized that different pelagic groups respond differently to effects of seamounts regarding their distribution and connectivity patterns. Herein, bacterial, protist, and fungal diversity was investigated across the water column around the Kocebu Guyot in the western Pacific Ocean. A higher connectivity was detected for bacteria than for protists and an extremely low connectivity for fungi, which might be attributed to parasitic and commensal interactions of many fungal taxa. The seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced protist connectivity along horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification. All the bacterial, protist, and fungal communities were more strongly affected by deterministic than stochastic processes. Drift appeared to have a more significant role in influencing the fungal community than other groups. Our study indicates the impact of seamounts on the pelagic community distribution and connectivity and highlights the mechanism of horizontally restricted dispersal combined with vertical mixing, which promotes the diversification of eukaryotic life.

A multiscale view of the Phanerozoic fossil record reveals the three major biotic transitions

The hypothesis of the Great Evolutionary Faunas is a foundational concept of macroevolutionary research postulating that three global mega-assemblages have dominated Phanerozoic oceans following abrupt biotic transitions. Empirical estimates of this large-scale pattern depend on several methodological decisions and are based on approaches unable to capture multiscale dynamics of the underlying Earth-Life System. Combining a multilayer network representation of fossil data with a multilevel clustering that eliminates the subjectivity inherent to distance-based approaches, we demonstrate that Phanerozoic oceans sequentially harbored four global benthic mega-assemblages. Shifts in dominance patterns among these global marine mega-assemblages were abrupt (end-Cambrian 494 Ma; end-Permian 252 Ma) or protracted (mid-Cretaceous 129 Ma), and represent the three major biotic transitions in Earth’s history. Our findings suggest that gradual ecological changes associated with the Mesozoic Marine Revolution triggered a protracted biotic transition comparable in magnitude to the end-Permian transition initiated by the most severe biotic crisis of the past 500 million years. Overall, our study supports the notion that both long-term ecological changes and major geological events have played crucial roles in shaping the mega-assemblages that dominated Phanerozoic oceans.

Rojas et al. present a new multi-scale model that reveals the three major biotic transitions of the Phanerozoic fossil record. This new model supports the hypothesis that both long-term ecological changes and major geological events played crucial roles in shaping ocean mega-assemblages through the Phanerozoic.

Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis

The aim of this study was to select a candidate deep-sea amphipod species suitable for connectivity analyses in areas around cobalt-rich ferromanganese crusts (CRCs). We applied DNA barcoding based on the mitochondrial protein-coding gene, cytochrome c oxidase subunit I (COI), to specimens collected from the Xufu Guyot (the JA06 Seamount) off southeastern Minami-Torishima Island in the North Pacific, where CRCs are distributed. We used baited traps to collect 37 specimens. Comparison of COI sequences with public reference databases (GenBank, BOLD) showed that almost all of the specimens belonged to the superfamily Lysianassoidea, which is known to be ubiquitous in deep-sea areas. In a molecular taxonomic analysis of these sequences, we detected 11 clades. One of these clades (group 9) composed of 18 sequences and was identified by DNA barcoding as a putative species belonging to Abyssorchomene, which has been reported from the New Hebrides Trench in the South Pacific. We considered this species to be a candidate for connectivity analysis and analyzed its genome by restriction site–associated DNA sequencing. The results showed that the genetic variation in this species is adequate for analyzing connectivity patterns in CRC areas in the future.

Variation in species diversity of deep-water megafauna assemblages in the Caribbean across depth and ecoregions

Diversity patterns of the deep-sea megafauna in the Caribbean Basin and the Guiana ecoregion were analyzed in order to test the hypothesis of species richness variation as a function of depth and the hypothesis of non-differences between ecoregions by analyzing spatial patterns of five taxa and a merged assemblage. Collections of five taxa (corals, sea stars, sea urchins, sea lilies and gastropods) were obtained from seven oceanographic expeditions aboard the R/V Pillsbury at 310 stations between 60 and 7500 m depth. Data were sorted according to depth zones and ecoregions and were analyzed in order to estimate species richness, changes in species composition and distinction of β-diversity by species turnover or by nestedness. The observed patterns of diversity were consistent between taxa and their assemblage: Species richness increased from the continental shelf (60-200 m deep) to the slope (200-2000 m deep), followed by a decrease at the continental rise-abyssal zone. We detected marked changes in species composition according to depth ranges. Changes in species composition in relation to ecoregions were also detected. In general, the Caribbean Basin lacks important physical barriers, causing high deep-sea ecosystem connectivity; however, variation in composition could be related to changes in environmental conditions associated with productivity and/or continental influences.

A new yeti crab phylogeny: Vent origins with indications of regional extinction in the East Pacific

The recent discovery of two new species of kiwaid squat lobsters on hydrothermal vents in the Pacific Ocean and in the Pacific sector of the Southern Ocean has prompted a re-analysis of Kiwaid biogeographical history. Using a larger alignment with more fossil calibrated nodes than previously, we consider the precise relationship between Kiwaidae, Chirostylidae and Eumunididae within Chirostyloidea (Decapoda: Anomura) to be still unresolved at present. Additionally, the placement of both new species within a new “Bristly” clade along with the seep-associated Kiwa puravida is most parsimoniously interpreted as supporting a vent origin for the family, rather than a seep-to-vent progression. Fossil-calibrated divergence analysis indicates an origin for the clade around the Eocene-Oligocene boundary in the eastern Pacific ~33–38 Ma, coincident with a lowering of bottom temperatures and increased ventilation in the Pacific deep sea. Likewise, the mid-Miocene (~10–16 Ma) rapid radiation of the new Bristly clade also coincides with a similar cooling event in the tropical East Pacific. The distribution, diversity, tree topology and divergence timing of Kiwaidae in the East Pacific is most consistent with a pattern of extinctions, recolonisations and radiations along fast-spreading ridges in this region and may have been punctuated by large-scale fluctuations in deep-water ventilation and temperature during the Cenozoic; further affecting the viability of Kiwaidae populations along portions of mid-ocean ridge.

Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems

BACKGROUND

A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies.

RESULTS

The review of microhabitats showed that many ampharetid species have a wide niche in terms of temperature and substratum. Depth may be limiting some species to a certain habitat, and trophic ecology and/or competition are identified as other potentially relevant factors. The phylogeny revealed that ampharetids have adapted into CBEs at least four times independently, with subsequent diversification, and shifts between ecosystems have happened in each of these clades. Evolutionary transitions are found to occur both from seep to vent and vent to seep, and the results indicate a role of sedimented vents in the transition between bare-rock vents and seeps.

CONCLUSION

The high number of ampharetid species recently described from CBEs, and the putative new species included in the present phylogeny, indicates that there is considerable diversity still to be discovered. This study provides a molecular framework for future studies to build upon and identifies some ecological and evolutionary hypotheses to be tested as new data is produced.

Marine biogeographic realms and species endemicity

Marine biogeographic realms have been inferred from small groups of species in particular environments (e.g., coastal, pelagic), without a global map of realms based on statistical analysis of species across all higher taxa. Here we analyze the distribution of 65,000 species of marine animals and plants, and distinguish 30 distinct marine realms, a similar proportion per area as found for land. On average, 42% of species are unique to the realms. We reveal 18 continental-shelf and 12 offshore deep-sea realms, reflecting the wider ranges of species in the pelagic and deep-sea compared to coastal areas. The most widespread species are pelagic microscopic plankton and megafauna. Analysis of pelagic species recognizes five realms within which other realms are nested. These maps integrate the biogeography of coastal and deep-sea, pelagic and benthic environments, and show how land-barriers, salinity, depth, and environmental heterogeneity relate to the evolution of biota. The realms have applications for marine reserves, biodiversity assessments, and as an evolution relevant context for climate change studies.

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls

Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time on the Eastern Mediterranean sunken wooden logs. This study suggests that biogeography and succession play an important role for the composition of bacteria and fauna of wood-associated communities, and that wood can act as stepping-stones for seep biota.