Diversity In Sediments Research Articles

Strong associations between dissolved organic matter and microbial communities in the sediments of Qinghai-Tibetan Plateau lakes depend on salinity

In aquatic ecosystems, dissolved organic matter (DOM) plays a vital role in microbial communities and the biogeochemical cycling of elements. However, little is known about the associations between DOM and microbial communities in lake sediments. This study investigated the composition of water-extractable organic matter and microbial communities in surface sediments of lakes with different salinities on the Qinghai-Tibet Plateau. Ultrahigh-resolution mass spectrometry and high-throughput microbial sequencing techniques were employed to assess the associations between molecular diversity and microbial diversity and the effects of salinity in 19 lakes spanning a salinity range from 0.22 ‰ to 341.87 ‰. Our results show that increasing salinity of lake water led to higher molecular diversity of DOM in surface sediments. High-salinity lakes exhibited distinct DOM characteristics, such as lower aromaticity, smaller molecular weight, and higher oxidation degree, compared to freshwater lakes. The complexity of the microbial network composition of sediments first increased and then decreased with the increase of salinity. Moreover, as salinity increases, the dominant species transitioned from Gammaproteobacteria to Bacteroidia, and this transition was accompanied by a decrease in microbial diversity and an increase in molecular diversity. Microbial factors accounted for 34.68 % of the variation in the molecular composition of DOM. Overall, this study emphasizes the significant effects of salinity on both molecular and microbial diversity in lake sediments. Furthermore, our findings underscore the importance of microbes in controlling the range of organic compounds present in lakes and deepen our knowledge of the biogeochemical cycling of DOM.

Microbial diversity in shallow-sea sediment from Tsukumo Bay, Japan, determined by 16S rRNA gene amplicon sequencing.

Information about the microbiota in marine sediments is important because the microbiota and their activities in sediments affect the surrounding marine environment. To evaluate the microbial diversity, we performed 16S rRNA gene amplicon sequencing on sediment samples from 19 stations in Tsukumo Bay, the northern area of Noto Peninsula, Japan.

Microbial community diversity of an integrated constructed wetland used for treatment of sewage.

The microbial community diversity in Constructed Wetland System (CWS) plays a key role in the removal of pollutants from waste water. An integrated functional CWS developed at Neela Hauz Biodiversity Park, Delhi was selected to assess the diversity in composition and structure of microbial community diversity of sludge and sediment of CWS, based on metagenomic approach using 16S rRNA genes. The sediment showed higher diversity than sludge and both formed distinct clusters. The taxonomic structure of the microbial community of CWS is represented by 6,731 OTUs distributed among 2 kingdoms, 103 phyla, 227 classes, 337 orders, 320 families, 295 identified genera, and 84 identified species. The relative abundance of top 5 dominant phyla of sludge and sediment varied from 3.77% (Acidobacteria) to 35.33% (Proteobacteria) and 4.07% (Firmicutes) to 28.20% (Proteobacteria), respectively. The range of variation in relative abundance of top 5 dominant genera of sludge and sediment was 2.58% (Hyphomicrobium) to 6.61% (Planctomyces) and 2.47% (Clostridium) to 4.22% (Syntrophobacter), respectively. The rich microbial diversity of CWS makes it perform better in pollutants removal (59.91-95.76%) than other CWs. Based on the abundance values of taxa, the taxa are grouped under four frequency distribution classes-abundant (>20), common (10-19), rare (5-9), and very rare (1-4). The unique structure of microbial communities of integrated CWS is that the number of abundant taxa decreases in descending order of taxonomic hierarchy, while the number of rare and very rare taxa increases. For example, the number of abundant phyla was 14 and 21 in sludge and sediment, respectively and both communities have only 3 abundant genera each. This is in contrast to 4 and 17 very rare phyla in sludge and sediment, respectively and both the communities have 114 and 91 very rare genera, respectively. The outcomes of the study is that the integrated CWS has much higher microbial community diversity than the diversity reported for other CWs, and the rich diversity can be used for optimizing the performance efficiency of CWS in the removal of pollutants from waste water. Such structural diversity might be an adaptation to heterogeneous environment of CWS.

Benthic and Planktonic Microalgae Community in Probolinggo Beach

Microalgae, micro-sized plant organisms, play a crucial role in aquatic ecosystems. While many microalgae inhabit substrates or the bottom of water bodies, several types are planktonic. This study aimed to identify the types and abundance of microalgae in both sediment and water column habitats, as well as to analyse the environmental factors influencing their abundance. The research encompasses observations of water quality factors, microalgae abundance, relative abundance, diversity index, evenness index, and dominance index. Statistical analyses were using non-metric multidimensional scaling (NMDS) and Canonical Correspondence Analysis (CCA). The study was conducted in May-June 2022, with bi-weekly sampling at three points within each location for two months. Microalgae identified in the coastal area of Probolinggo belong to the Bacillariophyceae, Cyanophyceae, and Chlorophyceae classes. The highest microalgae abundance in sediment habitat was 58,472 ind/cm2, while in the water column was 4,118 ind/l. Diversity, evenness, and dominance indices in both sediment and water column habitats ranged from 1.93 to 2.61, 0.88 to 0.98, and 0.09 to 0.10, respectively. NMDS and CCA analyses indicate a graphical representation of the Bacillariophyceae class, demonstrating its prevalence across all sites.

The effect of fermented feed (FF) on intestinal, surrounding water, and sediment microbiomes of the Chinese mitten crab Eriocheir sinensis

AbstractObjectiveFermented feed (FF) has several significant advantages in aquaculture. However, little is known about the characteristics of intestinal and environmental microbiota in the Chinese mitten crab Eriocheir sinensis.MethodsThis study was conducted to elucidate the relationship between bacterial communities in the intestine of Chinese mitten crabs and the surrounding environment and to compare the bacterial communities in FF and non‐FF diet modes by using 16S ribosomal RNA high‐throughput sequencing technology.ResultFermented feed diets mainly influenced the alpha diversity of intestinal microbiomes but could affect microbial community structures of beta diversity in water and sediment. Compared to water and sediment, crab intestines had the lowest operational taxonomic unit (OTU) richness and bacterial community diversity. The OTU richness and Chao richness index values were lower in the intestines of crabs that received FF than in crabs that were given non‐FF. No significant differences were observed in the bacterial diversity and OTU richness of water and sediment between the two feeding modes. The bacterial community structures were significantly different among the three environments. Tenericutes, Proteobacteria, and Actinobacteria were the most abundant phyla in the crab intestine, sediment, and water, respectively. Bacterial functions were also different among the three environments. Proportions of nitrate reduction and fermentation in the crab intestine, proportions of nitrification and sulfate respiration in the sediment, and proportions of chemoheterotrophy and aerobic chemoheterotrophy in the water were higher for the FF feeding mode than for the non‐FF mode.ConclusionThe bacterial community structures were significantly different among the three environments. The microbiome of the crab intestine was partially shared with that of the ambient environment. Additionally, the FF mainly influenced the alpha diversity of intestinal microbiomes but also affected the community structures of beta diversity in water and sediment. These results will help us to devise dietary strategies to influence the crab intestinal microbiota and provide guidance for sustainable crab culture practices.

Metazoan diversity and community assemblages in sediments across a Western Pacific Trench-Arc-Basin system: insights from eDNA metabarcoding

Trench-arc-basin (TAB) systems are widely distributed in the deep sea, yet our understanding of their biodiversity patterns and community assemblages remains limited. In this study, we collected sediment samples from 22 stations across a Western Pacific TAB system and identified 85 families of marine benthos from 15 phyla by using eDNA metabarcoding with the 18S rRNA gene V4 region. Nematodes were the most dominant metazoan taxa followed by echinoderms, arthropods, and annelids. The highest biodiversity and species specificity were observed at stations located near seamounts. The community assemblages were highly heterogeneous in this TAB system, likely induced by the large geographic barriers and the high habitat heterogeneity. Furthermore, the total organic carbon content and median grain size of the sediment drive the overall community composition, and the water depth exerts a significant influence on species richness and abundance. Our results provide insight into benthos diversity and distribution across a TAB system and data for further comparisons and modeling studies.

Prokaryotic Community Composition and Diversity in Sediments from Choctafaula, Uphapee, and Cubahatchee Creeks in the Lower Tallapoosa River Basin, Macon County, Alabama: An Observational Study

Sedimentary prokaryotes are primarily responsible for metabolic activity in rivers. They are subjected to a variety of natural and anthropogenic pressures, allowing us to use the composition and diversity of their communities as indicators of ecological health. For our investigation, we looked at sediments from three ecologically critical streams in the Lower Tallapoosa River Basin (Choctafaula, Uphapee, and Cubahatchee Creeks). The prokaryotic community was characterized using molecular approaches, and elemental concentrations were determined by inductively coupled plasma atomic emission spectrometry. This research demonstrated that Proteobacteria (45.02–80.73%), Bacteroidetes (1.98–26.52%), Firmicutes (1.36–50.67%), Actinobacteria (1.55–16.81%), and Acidobacteria (0.13–8.77%) were the most prevalent phyla. Key physicochemical parameters, core communities at multiple taxonomic levels, and several pathogenic genera shifted radically between streams. Weighted and unweighted unifrac distance metrics based PCoA plots indicated the structural and membership similarity of samples from specific creek ecosystems. Based on our research findings, it is evident that the composition and diversity of prokaryotic communities in sediment could serve as significant indicators in stream ecosystems. Further investigation and application of these indicators could prove valuable in assessing the health of streams, particularly in light of the accelerated changes resulting from climate change within a condensed timeframe.

Evaluation of Fungal Diversity in Water and Sediment, AgbaNdele Segment, Sombriero River, Rivers State

This study was carried out between September and December, 2022 in Sombriero river to assess the water and sediment quality using fungal load and diversity. Water and sediment samples collected were analysed in the laboratory for fungi using standard method of APHA and the obtained data were subjected to descriptive and inferential statistics. The results showed that Total fungi in water (Tfw) and sediment (TFs) ranged from 1.0x101 to 1.4x102cfu/ml and 1.0x101 to 1.7x102cfu/g with the overall mean values of 114.37±35.397 cfu/ml and 168.44±358.999 cfu/g respectively. Spatial mean values of TFw and TFs varies significantly at p<0.05 with station 3 higher than all other stations. TFw and TFs values exhibited non-seasonality and seasonality respectively at p<0.05. The total of 5 and 6 fungal species observed in the water and sediment samples included Aspergillus niger, Rhizopus oligospora, Pennicilium species, Mucoccus caris and Micrococcus caris with Fusarium solani absent in water. The values of diversity indices varied spatially with Simpson’s dominance index (D) of fungi in water ranging between 0.2503 and 0.6428 while that of sediment ranged from 0.255 to 0.609. Based on the fungal load, diversity index and some pathogenic species the water is therefore under stress/threat. There is need to regulate the anthropogenic activities in the area to avoid further discharge of wastes capable of causing further pollution of the area.

Diversity and novel lineages of black yeasts in Chaetothyriales from freshwater sediments in Spain.

Black yeasts comprise a group of Ascomycota of the order Chaetothyriales with highly variable morphology, a great diversity of ecological niches and life cycles. Despite the ubiquity of these fungi, their diversity in freshwater sediments is still poorly understood. During a survey of culturable Ascomycota from river and stream sediments in various sampling sites in Spain, we obtained 47 isolates of black yeasts by using potato dextrose agar supplemented with cycloheximide. A preliminary morphological study and sequence analyses of the internal transcribed spacer region (ITS) and the large subunit (LSU) of the nuclear rDNA revealed that most of the isolates belonged to the family Herpotrichiellaceae. We have confidently identified 30 isolates representing the following species: Capronia pulcherrima, Cladophialophora emmonsii, Exophiala equina, Exophiala pisciphila, Exophiala radicis, and Phialophora americana. However, we encountered difficulty in assigning 17 cultures to any known species within Chaetothyriales. Combining phenotypic and multi-locus phylogenetic analyses based on the ITS, LSU, β-tubulin (tub2) and translation elongation factor 1-α (tef1-α) gene markers, we propose the new genus Aciculomyces in the Herpotrichiellaceae to accommodate the novel species Aciculomyces restrictus. Other novel species in this family include Cladophialophora denticulata, Cladophialophora heterospora, Cladophialophora irregularis, Exophiala candelabrata, Exophiala dehoogii, Exophiala ramosa, Exophiala verticillata and Phialophora submersa. The new species Cyphellophora spiralis, closely related to Cyphellophora suttonii, is described, and the phylogeny of the genus Anthopsis in the family Cyphellophoraceae is discussed. By utilizing these four markers, we were able to strengthen the phylogenetic resolution and provide more robust taxonomic assessments within the studied group. Our findings indicate that freshwater sediments may serve as a reservoir for intriguing black yeasts, which warrant further investigation to address gaps in phylogenetic relationships, particularly within Herpotrichiellaceae. Citation: Torres-Garcia D, García D, Réblová M, et al. 2023. Diversity and novel lineages of black yeasts in Chaetothyriales from freshwater sediments in Spain. Persoonia 51: 194-228. doi: 10.3767/persoonia.2023.51.05.

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.

Chemodiversity of riverine dissolved organic matter: Effects of local environments and watershed characteristics

Riverine dissolved organic matter (DOM) is crucial to global carbon cycling and aquatic ecosystems. However, the geographical patterns and environmental drivers of DOM chemodiversity remain elusive especially in the waters and sediments of continental rivers. Here, we systematically analyzed DOM molecular diversity and composition in surface waters and sediments across 97 broadly distributed rivers using data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium. We further examined the associations of molecular richness and composition with geographical, climatic, physicochemical variables, as well as the watershed characteristics. We found that molecular richness significantly decreased toward higher latitudes, but only in sediments (r = -0.24, p < 0.001). The environmental variables like precipitation and non-purgeable organic carbon showed strong associations with DOM molecular richness and composition. Interestingly, we identified that less-documented factors like watershed characteristics were also related to DOM molecular richness and composition. For instance, DOM molecular richness was positively correlated with the soil sand fraction for waters, while with the percentage of forest for sediments. Importantly, the effects of watershed characteristics on DOM molecular richness and composition were generally stronger in waters than sediments. This phenomenon was further supported by the fact that 11 out of 13 watershed characteristics (e.g., the percentages of impervious area and cropland) showed more positive than negative correlations with molecular abundance especially in waters. As the percentage of forest increased, there was a continuous accumulation of the compounds with higher molecular weight, aromaticity, and degree of unsaturation. In contrast, human activities accumulated the compounds with lower molecular weight and oxygenation, and higher bioavailability. Our findings imply that it may be possible to use a small set of broadly available data types to predict DOM molecular richness and composition across diverse river systems. Elucidation of mechanisms underlying these relationships will provide further enhancements to such predictions, especially when extrapolating to unsampled systems.

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

BackgroundLeakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.ResultsIn this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.ConclusionREMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data.8PNdJCR5n5eFCnFqsf6X4UVideo

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort

Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.

Active microeukaryotes hold clues of effects of global warming on benthic diversity and connectivity in the coastal sediments

The marine flora and fauna along the China seas include the Indo-West Pacific warm-water fauna and the North Pacific temperate fauna. The latitude of 32°N is recognized as the ecological barrier for benthic fauna in the China Seas. However, the ecological barrier on macrobenthos community gradually weakened because of global warming. Microeukaryotes are major components of marine food webs and can quickly response to environmental changes. We hypothesis that microeukaryotic benthos can stride over the ecological barrier of 32°N from the East China Sea (ECS) to the Yellow Sea (YS) under the global change, but their distribution is still limited by depth gradients between the South China Sea (SCS) and the ESC. Therefore, we investigated the distribution of benthic microeukaryotes in the China Seas using RNA metabarcoding. Higher OTU richness and phylogenetic diversity were detected in the SCS than those in the YS and ECS. The YS and ECS communities clustered together firstly and then clustered with the SCS community. Unexpectedly, communities from the 33°N in the YS clustered with those from the ECS. Similar pattern was also detected for Cercozoa, Diatomea, Amoebozoa and Fungi. These findings indicated that microeukaryotic benthos strode over the ecological barrier of 32°N under the global change. Source-sink analyses indicated more than 50% sources of the 33°N community were attributed to the ECS community, while only 12.5% from the YS community. Depth, temperature and latitude showed significant influence on communities in the China Seas. This study highlights the response of active microeukaryotes to the global warming in the coastal sediments.

Unraveling the genomic diversity and ecological potential of the genus Demequina: insights from comparative analysis of different saline niche strains

During an investigation of the culturable microbial diversity of sediments with salinity from tidal flats and saline lake, seven strains of the genus Demequina were harvested. The genomic analysis and physiological characteristics of strains of this genus have unveiled their significant potential in degrading complex carbon source such as lignin, hemicellulose, chitin, and oligosaccharides. In addition, these strains show potential abilities in nitrite ammonification and sulfide oxidation. These findings not only improved our understanding of their metabolic model, but also provided valuable insights into their ecological roles. Four new species of the genus Demequina are described: Demequina litoralis sp. nov., with SYSU T00192T designated as the type species; Demequina zhanjiangensis sp. nov., with SYSU T00b26T as the type species; Demequina lignilytica sp. nov., with SYSU T00068T as the type species; and Demequina muriae sp. nov., with EGI L300058T as the type species. Additionally, strains SYSU T0a273, SYSU T00039-1, and SYSU T00039 are identified as different strains of Demequina lignilytica. Our study thus sheds light on the diversity, biological significance, and ecological contribution of the Demequina genus in different habitats.

Physicochemical Properties and Bacterial Diversity of Sediment in Sea Cucumber Culture Ponds under High Summer Temperatures

This study examined the effect of aquaculture management parameters on sea cucumbers in culture ponds during high summer temperatures. The physicochemical properties of 18 sediment samples from six sea cucumber culture ponds were assessed at a high temperature (HT) and the end of the high temperature (EHT) stages of summer. High-throughput sequencing was used to analyze the bacterial community composition and diversity of the sediment in the culture pond. The results showed that total nitrogen (TN), total carbon (TC), total organic carbon (TOC), ammonia nitrogen (NH4+), total sulfur (TS), sulfate (SO42−), and sulfide (S2−) contents were the lowest in the Geziling sediments at both stages, indicating a favorable sediment environment. The TN, TC, TOC, and NH4+ contents decreased significantly in the Wulei Island sediments during the EHT stage, indicating strong self-purification capacity. The TN, TC, TOC, NH4+, TS, SO42−, and S2− were higher in the Rushankou and Xiaohongcun sediments during both stages, indicating a worse sediment environment. Alpha diversity analysis revealed increased bacterial diversity in the sediments during the HT stage when compared to that during the EHT stage. Correlation analysis between bacterial diversity and the physicochemical properties of the TN sediments had the greatest impact on bacterial diversity, followed by TOC, TC, NH4+, TS, S2−, SO42−, and NO2− (in order). Our results suggest that the physicochemical properties (TC, TOC, TN, and NH4+) of the culture pond sediment can significantly influence bacterial community composition and diversity. Management measures for aquaculture, including desilting and monthly water change, could positively affect these physicochemical properties and the bacterial community structure of the sediment. These findings will provide a reference for healthier aquaculture practices of Apostichopus japonicus under high summer temperatures.

Unveiling the ecological significance of phosphorus fractions in shaping bacterial and archaeal beta diversity in mesotrophic lakes.

Both community variation and phosphorus (P) fractions have been extensively studied in aquatic ecosystems, but how P fractions affect the mechanism underlying microbial beta diversity remains elusive, especially in sediment cores. Here, we obtained two sediment cores to examine bacterial and archaeal beta diversity from mesotrophic lakes Hongfeng Lake and Aha Lake, having historically experienced severe eutrophication. Utilizing the Baselga's framework, we partitioned bacterial and archaeal total beta diversity into two components: species turnover and nestedness, and then examined their sediment-depth patterns and the effects of P fractions on them. We found that total beta diversity, species turnover or nestedness consistently increased with deeper sediment layers regarding bacteria and archaea. Notably, there were parallel patterns between bacteria and archaea for total beta diversity and species turnover, which is largely underlain by equivalent processes such as environmental selection. For both microbial taxa, total beta diversity and species turnover were primarily constrained by metal oxide-bound inorganic P (NaOH-Pi) and sediment total phosphorus (STP) in Hongfeng Lake, while largely affected by reductant-soluble total P or calcium-bound inorganic P in Aha Lake. Moreover, NaOH-Pi and STP could influence bacterial total beta diversity by driving species nestedness in Hongfeng Lake. The joint effects of organic P (Po), inorganic P (Pi) and total P fractions indicated that P fractions are important to bacterial and archaeal beta diversity. Compared to Po fractions, Pi fractions had greater pure effects on bacterial beta diversity. Intriguingly, for total beta diversity and species turnover, archaea rather than bacteria are well-explained by Po fractions in both lakes, implying that the archaeal community may be involved in Po mineralization. Overall, our study reveals the importance of P fractions to the mechanism underlying bacterial and archaeal beta diversity in sediments, and provides theoretical underpinnings for controlling P sources in biodiversity conservation.

Microbial diversity and authigenic siderite mediation in sediments surrounding the Kedr-1 mud volcano, Lake Baikal.

The gas hydrate-bearing structure-mud volcano Kedr-1 (Lake Baikal, southern basin)-is located near the coal-bearing sediments of the Tankhoy formation of Oligocene-Miocene age and can be an ideal source of gas-saturated fluid. A significant amount of siderite minerals (FeCO3 ) were collected from sediments at depths ranging from 0.5 to 327 cm below the lake floor (cmblf). An important feature of these carbonate minerals is the extremely strong enrichment in the heavy 13 C isotope, reaching values of +33.3‰ VPDB. The δ13 C of the siderite minerals, as well as their morphology and elemental composition, and the δ13 CDIC of the co-existing pore water, differed across layers of the core, which implies at least two generations of siderite formation. Here, we leverage mineralogical and geochemical data with 16S rRNA data from the microbial communities in sediments surrounding layers containing siderite minerals. Statistical data reveal the formation of three clusters of microbial communities based on taxonomical composition, key taxa among bacteria and archaea, and environmental parameters. Diversity and richness estimators decrease with sediment depth, with several similar prevailing clades located at the bottom of the core. Most of the taxa in the deep sediments could be associated with putative metabolisms involving organotrophic fermentation (Bathyarchaeia, Caldatribacteriota, and Chloroflexota). Various groups of methanogens (Methanoregulaceae, Methanosaetaceae, and Methanomassiliicoccales) and methanotrophic (Methanoperedenaceae) archaea are present in the sediment at variable relative abundances throughout the sampled depth. Based on the physicochemical characteristics of the sediment, carbon isotope analysis of carbonate minerals and DIC, and phylogenetic analysis of individual taxa and their metabolic potential, we present several models for subsurface siderite precipitation in Lake Baikal sediments.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China.

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer

Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer