东太结核主要为半埋藏和埋藏型,发育于以黏土和硅质组分为主的沉积环境。东太结核的锰相矿物主要有水羟锰矿和钡镁锰矿,具有较高的REY、Cu、Ni含量和Mn/Fe比值,显示遭受间隙水的影响,落入水成成因和成岩成因两个区间范围。西太结核主体暴露在海水中,周围沉积物主要由深海黏土组成。西太结核的锰相矿物几乎只有水羟锰矿,具有较高的REY、Co含量和低Mn/Fe比值,属于典型的水成成因型。两个区域的多金属结核的稀土北美页岩标准化模式均显示Ce正异常、Y负异常和无或弱Eu异常,与海水稀土特征构成良好的耦合关系,是多金属结核对海水稀土选择性富集的结果。西太结核相对东太结核具有更高的Ce含量和δCe,Co、Ti与Ce具有良好的正相关关系。研究认为海水中溶解氧并不一定是控制结核Ce正异常程度的关键因素,Co、Ti等元素及其相关组分能够引起Ce与其他稀土元素的强烈分馏,也可能是影响多金属结核Ce正异常程度的控制因素。研究区多金属结核和富钴结壳表层样的ε_Nd范围为-6.6~-2.5,是全球最富放射性成因Nd的海洋铁锰壳层。结合稀土模式以及Eu异常特征,本研究认为多金属结核的稀土主要来自ε_Nd相对较高的周围陆壳,可以通过河流或者大气沉降等方式输送到大洋,而研究区广泛分布的海山玄武岩释放的放射性成因Nd同位素对海水的影响微弱。

The polymetallic nodules in China’s polymetallic nodules exploration contract area in the East Pacific Basin (EP nodules) are largely buried or semi-buried in a sedimentary environment dominated by clay and siliceous components. The manganese mineral phases of the EP nodules mainly include vernadite and todorokite, with high REY and high Cu and Ni contents and Mn/Fe ratio. These characteristics indicate the nodules are affected by interstitial water thus falling into the range of diagenesis and hydrogenesis. In comparison, the polymetallic nodules in the Northwest Pacific Basin (WP nodules) are mostly exposed to seawater, and the surrounding sediments are mainly deep-sea clay. The manganese mineral phases of the WP nodules are almost all vernadite, with high REY, high Co content and low Mn/Fe ratio. It shows that the WP nodules are of typical hydrogenic form. The NASC-normalized REY patterns of the polymetallic nodules in both regions show positive Ce and negative Y anomalies and no/weak Eu anomaly, while the REY patterns of ambient seawater show obvious negative Ce and positive Y anomalies and no obvious Eu anomaly. This inverse coupling relationship implies that the REY patterns of the polymetallic nodules are the result of selective enrichment from seawater. The WP nodules have higher Ce content and δCe than the EP nodules. Both Co and Ti correlate positively with Ce, which may collectively affect the selection of Ce and Y in seawater by polymetallic nodules. In this study, dissolved oxygen in seawater was not a factor controlling the level of positive Ce anomaly observed in the polymetallic nodules. Rather, elements such as Co and Ti and their related components can cause strong fractionation of Ce and other REY, which may be the controlling factor. The surface samples of polymetallic nodules and cobalt-rich crusts in the study area, with ε_Nd values ranging from -6.6 to -2.5, represent the most radioactive ferromanganese samples of Nd in the global sea area. Combining the ε_Nd result with REY patterns and Eu anomaly, we suggest that REY in polymetallic nodules mainly come from the surrounding continental crust with relatively high ε_Nd and can be transported to the ocean via rivers or atmospheric deposition. However, the radioactive Nd isotopes released from basalt in the Northwest Pacific Basin have only weak effect on the seawater.

Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.© 2023. The Author(s).

Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.Copyright © 2019 Elsevier Ltd. All rights reserved.

Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats.Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes.Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.© 2024. The Author(s).

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the alpha-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment.

The Deepwater Horizon incident in the Gulf of Mexico in 2010 released an unprecedented amount of petroleum hydrocarbons 1500 meters below the sea surface. Few studies have considered the influence of hydrostatic pressure on bacterial community development and activity during such spills. The goal of this study was to investigate the response of indigenous sediment microbial communities to the combination of increased pressure, hydrocarbons and dispersant. Deep-sea sediment samples collected from the northern Gulf of Mexico were incubated at atmospheric pressure (0.1 MPa) and at elevated pressure (10 MPa), with and without the addition of crude oil and dispersant. After incubations at 4 °C for 7 days, Colwellia and Psychrobium were highly abundant in all samples. Pressure differentially impacted members of the Alteromonadales. The influences of pressure on the composition of bacterial communities were most pronounced when dispersant was added to the incubations. Moritella and Thalassotalea were greatly stimulated by the addition of dispersant, suggesting their roles in dispersant biodegradation. However, Moritella was negatively impacted by increasing pressure. The presence of dispersant was shown to decrease the relative abundance of a known hydrocarbon degrader, Cycloclasticus, while increasing pressure increased its relative abundance. This study highlights the significant influence of pressure on the development of microbial communities in the presence of oil and dispersant during oil spills and related response strategies in the deep sea.

Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.

The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions, and organic matter inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Thermodesulfobacteriota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.© 2022. The Author(s).

Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about the biotic composition, origins, and variability of sinking particles reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured and preserved in sediment traps at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9-month time-series, Bacteria dominated both the rRNA-gene and rRNA pools, followed by eukaryotes (protists and animals) and trace amounts of Archaea. Deep-sea piezophile-like Gammaproteobacteria, along with Epsilonproteobacteria, comprised >80% of the bacterial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) and metazoa (predominantly pelagic mollusks and cnidarians) were the most common sinking particle-associated eukaryotes. Some near-surface water-derived eukaryotes, especially Foraminifera, Radiolaria, and pteropods, varied greatly in their abundance patterns, presumably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the prevalence of their nitrogen cycling-associated gene transcripts, suggested a central role for these bacteria in the mineralization and biogeochemical transformation of sinking particulate organic matter in the deep ocean. Our data also reflected several different modes of particle export dynamics, including summer export, more stochastic inputs from the upper water column by protists and pteropods, and contributions from sinking mid- and deep-water organisms. In total, our observations revealed the variable and heterogeneous biological origins and microbial activities of sinking particles that connect their downward transport, transformation, and degradation to deep-sea biogeochemical processes.Copyright © 2019 the Author(s). Published by PNAS.

Mustard tuber wastewater (MTWW) was used as both anolyte and catholyte in biocathode microbial fuel cell (BMFC). The results showed simultaneous nutrient and carbon removal and electricity generation were realized in BMFC. Excellent Chemical Oxygen Demand (COD) removal occurred in both anode (>90%) and cathode (>91%). Concerning nutrient removal, it was mainly removed in cathode. The maximum total phosphorus (TP) removal could reach 80.8 ± 1.0% by biological action. Simultaneous nitrification and denitrification (SND) was realized in cathode. The bacteria involved in nitrification were Nitrosomonas and SM1A02. Oceanimonas and Saprospiraceae_uncultured (anaerobic denitrifier), Thauera, Stenotrophomonas, Flavobacterium and Marinobacter (aerobic denitrifier), and Thioalkalispira (autotrophic denitrifier) were responsible for denitrification. Considering slight variation of anode and cathode pH, it could be concluded that MTWW was adequately self-buffered when used as electrolyte. Furthermore, electricity generation decreased with cathodic dissolved oxygen (DO) declining. These findings provide a novel method for MTWW resourceful treatment.Copyright © 2018 Elsevier Ltd. All rights reserved.

Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark oxygenated ocean and provides new perspective on carbon cycling in the ocean's largest habitat.

Continuous-flow cell systems were used to cultivate a degradative biofilm community with the herbicide diclofop methyl as the sole carbon and energy source. The aromatic character of this compound and its breakdown products enabled direct visualization of their accumulation in the biofilm matrix. This accumulation could be inhibited by addition of a more labile carbon source to the culture medium or by inhibition of cell activity. The fluorescence of diclofop-grown biofilms remained constant after 14 to 21 days but decreased with time when diclofop was omitted from the irrigation solution. However, this decrease was inhibited by cyanide, indicating either utilization or release of accumulated diclofop when the cells were viable. Subsequent experiments with [(sup14)C]diclofop also indicated that decreased fluorescence in the absence of an exogenous carbon source resulted from degradation of adsorbed diclofop and its breakdown products by the biofilm bacteria. These results demonstrate that biofilm exopolymers can facilitate storage of nutrients for subsequent mineralization during periods of carbon limitation.

Deep sea minerals in polymetallic nodules, crusts and hydrothermal vents are not only formed by mineralization but also by biologically driven processes involving microorganisms (biomineralization). Within the nodules, free-living and biofilm-forming bacteria provide the matrix for manganese deposition, and in cobalt-rich crusts, coccolithophores represent the dominant organisms that act as bio-seeds for an initial manganese deposition. These (bio)minerals are economically important: manganese is an important alloying component and cobalt forms part of special steels in addition to being used, along with other rare metals, in plasma screens, hard-disk magnets and hybrid car motors. Recent progress in our understanding of the participation of the organic matrices in the enrichment of these metals might provide the basis for feasibility studies of biotechnological applications.