Geographical distribution and driving force of micro-eukaryotes in the seamount sediments along the island arc of the Yap and Mariana trenches

IMPORTANCE

A distinct distribution pattern was shaped by a deterministic process. Enhanced vertical connectivity expanded the previous understanding of seamount effects. Parasitism and predation were prevalent in the seamounts.

The complete mitochondrial genome of deep-sea ophiuroid Ophioleila elegans (Echinodermata: Ophiuroidea) from the Shkolnik Guyot, a northwest Pacific seamount

Ophiuroids are a diversified benthic taxon in the deep sea. Given their various dispersal strategies, they are considered an adequate group to assess genetic connectivity, especially in the seamounts that function as islands. Ophioleila elegans A.H. Clark, 1949, in the family Ophiothamnidae, was previously reported from the Caiwei Guyot, a seamount in the northwest Pacific Ocean. Here, we described the mitochondrial genome of O. elegans collected from another seamount in the northwest Pacific. The whole mitogenome is 16,376 bp in length and encodes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on the mitogenome sequences showed that O. elegans was clustered with Histampica sp., the only species for which mitogenome sequence has been reported within the family Ophiothamnidae. The complete mitogenome of O. elegans first reported in the present study provides useful information for population genetics and evolutionary relationship of this taxon, especially in the northwest Pacific seamounts.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter

A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-M^T and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-M^T grew between 25 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l^-1 NaCl (optimum, 15-20 g l^-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l^-1 NaCl (optimum, 15-25 g l^-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H₂ as the primary electron donor, CO₂ as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-M^T and HR-1, respectively. Fe(OH)₃, MnO₂, AsO₄ ^3-, SO₄ ^2-, SeO₄ ^2-, S₂O₃ ^2-, S⁰ and NO₃ ^- were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-M^T and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii, within the class δ-Proteobacteria (now within the class Desulfuromonadia). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-M^T (=JCM 32109^T=KCTC 15831^T=ATCC TSD-173^T) and strain HR-1 (=JCM 32110=KCTC 15832).

Morphology and phylogenetic analysis of five deep-sea golden gorgonians (Cnidaria, Octocorallia, Chrysogorgiidae) in the Western Pacific Ocean, with the description of a new species

Explorations of seamounts in the Western Pacific Ocean and South China Sea resulted in collecting 18 specimens of golden gorgonians. Based on the morphology and the genetic analysis of mtMutS, they are described as one new species, Chrysogorgiacarolinensissp. nov., and four known species, including Chrysogorgiadendritica Xu, Zhan & Xu, 2020, Metallogorgiamelanotrichos (Wright & Studer, 1889), Metallogorgiamacrospina Kükenthal, 1919, and Pseudochrysogorgiabellona Pante & France, 2010. Chrysogorgiacarolinensis belongs to the Chrysogorgia “group A, Spiculosae” with rods or spindles distributed in the polyp-body wall and tentacles, and differs from all of its congeners except C.dendritica by the 1/3L branching sequence and amoeba-shaped sclerites at the basal polyp body. The mtMutS sequence of C.carolinensissp. nov. has six deletion mutations compared to those of its congeners, supporting the establishment of the new species. Although no genetic variability was observed between the closely related species C.dendritica and C.abludo Pante & Watling, 2012, the former is different from the latter by the apparently irregular sclerites in the polyp body wall. The two specimens of Metallogorgiamelanotrichos match well with the original description except for relatively larger polyps, while the M.macrospina specimens have slightly smaller polyps than the holotype. The juvenile of Metallogorgia has an obvious morphological difference with the adults in the colony shape and branches, but they can be unified by the same polyps and sclerites as well as mitochondrial MutS sequences. Thus, the generic diagnosis of Metallogorgia is slightly extended to include the morphology of juveniles. The morphology of Pseudochrysogorgiabellona Pante & France, 2010, as a new record for the South China Sea, matches well with that of the original description. In the phylogenetic trees, the Chrysogorgia species are separated into two clades, and while Metallogorgia and Pseudochrysogorgia formed a sister clade.

Seabed mining could come at a high price for a unique fauna

The deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep-sea ecosystems are urgently needed to establish a baseline prior to mining. However, significant gaps in our taxonomic knowledge and the high cost of sampling in the deep sea limit the effectiveness of conventional morphology-based surveys. In this issue of Molecular Ecology, Laroche et al. (Mol Ecol, 2020) capitalize on high throughput molecular methods to conduct one of the most detailed and rigorous surveys of the composition and biogeography of deep-seafloor metazoan communities to date. The authors show that deep seamounts in the Clarion Clipperton Zone are inhabited by rich metazoan communities that are distinct from those of the surrounding abyssal plains. These results have important conservation implications: if communities on deep seamounts were to persist after large-scale industrial mining operations on the surrounding plains, the seamounts would not serve as appropriate reservoirs to repopulate impacted areas.

nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount

The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7-8, 25-30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C_15 : 0 and summed feature 1 (composed of C_13 : 03-OH and/or iso-C_15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4^T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4^T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531^T (95.1 %) and Flagellimonas flava A11^T (93.9 %). Genome sequencing revealed the strain TP-CH-4^T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4^T represents a novel species of a novel genus of the family Flavobacteriaceae, for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4^T (=CGMCC 1.17120^T=KCTC 72434^T).

nov., isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390^T was related to the genus Flavobacterium and had highest 16S rRNA gene sequence identity with the type strain of Flavobacterium jejuense EC11^T (97.8 %). Sequence similarities to all other type strains of current species of the genus Flavobacterium were below 97 %. The predominant cellular fatty acids were iso-C_15 : 0 and iso-C_15 : 1G. The quinone system for strain TP390^T comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390^T was 31.2 mol%. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain TP390^T with F. jejuense KCTC 42149^T were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI data demonstrated that the strain TP390^T is representative of a novel species of the genus Flavobacterium, for which we propose the name Flavobacterium profundi sp. nov. (type strain TP390^T=KACC 18559^T=CGMCC 1.15398^T).

The complete mitochondrial genome of a deep sea ophiuroid of the genus Amphiura (Ophiuroidea: Amphiuridae)

Amphiura is a widely distributed genus of Ophiuroidea from various environment, play an important role in evolution. Here, we reported a complete mitochondrial genome of Amphiura sp. which was collected from a deep sea seamount in the West Pacific. The mitogenome is 15,457 in length, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. All genes are arranged in the same order of published mitogenomes in the same genus. The phylogenetic analysis support monophyly of the family Amphiuridae but not for the genus Amphiura.

isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YM155^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YM155^T was related to the genus Thalassotalea and had highest 16S rRNA gene sequence similarities with the type strains of Thalassotalea piscium T202^T (97.2 %) and Thalassotalea agariperforans M-M1^T (97.2 %). The predominant cellular fatty acids were C17 : 1ω8c, summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C16 : 0. Ubiquinone 8 (Q-8) was the respiratory quinone. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and one unidentified lipid. The genomic DNA G+C content of strain YM155^T was 36.1 mol%. On the basis of the evidence presented in this study, strain YM155^T represents a novel species of the genus Thalassotalea, for which we propose the name Thalassotalea profundi sp. nov. (type strain YM155^T=KACC 18563^T=CGMCC 1.15922^T).

Metazoan parasite communities and diet of the velvet belly lantern shark Etmopterus spinax (Squaliformes: Etmopteridae): a comparison of two deep-sea ecosystems

By combining an examination of stomach contents yielding a snapshot of the most recent trophic niche and the structure of parasite communities reflecting a long-term feeding niche, this study aimed at gaining more comprehensive information on the role of the small-sized deep-water velvet belly lantern shark Etmopterus spinax in the local food webs of the Galicia Bank and the canyon and valley system of the Avilés Canyon, which have been both proposed for inclusion in the Natura 2000 network of protected areas. As far as is known, this study provides the first comparative parasite infracommunity data for a deep-sea shark species. Component parasite communities in E. spinax were relatively rich, whereas the infracommunities were rather depauperate, with similar low diversity at both localities. The significant differences in the composition and structure of both parasite communities and prey assemblages indicate differential effects of the two deep-sea ecosystems on both long-term and most recent trophic niches of E. spinax. These results underline the importance of the use of multivariate analyses for the assessment of geographical variation in shark populations based on parasites and diet data.

Guadalupian (Middle Permian) giant bivalve Alatoconchidae from a mid-Panthalassan paleo-atoll complex in Kyushu, Japan: A unique community associated with Tethyan fusulines and corals

Unique new fossil assemblages containing the large bivalve family Alatoconchidae are recorded from the Guadalupian (Middle Permian) shallow marine limestone in Kamura, Kyushu. The large bivalves occur in the Neoschwagerina Zone and Lepidolina Zone. This discovery establishes that the biostratigraphic range of the family Alatoconchidae extends up to the top of the Lepidolina Zone (upper Capitanian of upper Guadalupian) i.e., to the end-Guadalupian extinction level. The largest Alatoconchidae in Kamura occurs in the Neoschwagerina Zone, the size of which is up to 50 cm long and 5 cm thick. Although details are still unknown, their morphology with a wing-like side projection of their valves appears very similar to that of Alatoconchidae that includes the well-known genus Shikamaia Ozaki. The bivalve-bearing Iwato Formation was derived from a mid-oceanic shallow marine carbonate build-up formed on a mid-oceanic paleo-seamount. The close association among the Alatoconchidae, typical Tethyan fusulines (Verbeekinidae) and rugose corals (Waagenophyllidae), plus their common extinction pattern suggests that the Alatoconchidae flourished in warm, shallow (photic) marine environments in low latitude areas in Panthalassa as well as Tethys. The extra-large size and double-layered shell with a translucent outer layer composed of prismatic calcite suggests that these bivalves may have hosted abundant photosynthetic algal symbionts to support their large-body metabolism.