Microbial Communities Involved in Methane, Sulfur, and Nitrogen Cycling in the Sediments of the Barents Sea

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.

In vivo toxicity of upconversion nanoparticles (NaYF4:Yb, Er) in zebrafish during early life stages: Developmental toxicity, gut-microbiome disruption, and proinflammatory effects

Lanthanide-doped upconversion nanoparticles (Ln-UCNPs) have been considered promising materials for various fields, such as biomedical and industrial applications. However, data and reports regarding its toxicity and environmental risks are scarce. Under these circumstances, data must be obtained to fully understand potential toxicity and adverse outcome pathways. In the present study, the toxicity of uncoated Ln-UCNP cores (NaYF4:Yb, Er) was systematically assessed in zebrafish embryos during early developmental stages. Ln-UCNPs were found to have multiple toxic effects, such as effects on survival rates, delayed hatching times, shorter body lengths, altered heart rates and blood circulation (significantly reduced), and neurobehavioral impairments in response to photoperiod stimulation. Bioimaging showed that Ln-UCNPs were distributed on the chorion, eyes, and skin at 72 hpf. However, it accumulates in the pharynx, esophagus, and intestine after oral administration. Ln-UCNPs disrupt the diversity and abundance of host-associated microorganisms (gut microbiota) leading to an increase in the prevalence of harmful bacteria in zebrafish. Transcriptomic and Ingenuity Pathway Analysis (IPA) predicted Interleukin-8 (IL-8) signaling, neuroinflammation, cardiac hypertrophy signaling pathways, immune and inflammation-related response interferon-gamma (ifnγ), and miR-155 as key mediators in regulatory effects. Based on this, a causal network was built showing the strong links between the induced gene expression of differentially expressed genes (DEGs), such as nitric oxide synthase 2 (nos2) and tumor necrosis factor (tnf) upon Ln-UCNPs treatment, and with the downstream adverse outcomes, in particular, the promotion of apoptosis, liver damage, and inflammatory response. Finally, RT-qPCR analysis confirmed the up-regulated expression of nos2 and tnf in the exposed larvae, consistent with the observation of an increased number of fluorescence-labelled neutrophils and macrophages in lyz: DsRed transgenic zebrafish until 120 hpf exposure, which together demonstrated the proinflammatory effects of Ln-UCNPs on organisms. In conclusion, we illustrated the developmental toxicity, disruption of gut-microbiome, and proinflammatory effects of Ln-UCNP cores on zebrafish, and the causal network from IPA analysis may help further elucidate the adverse outcome pathway of Ln-UCNPs.

Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea

Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3--N, NO2--N, PO43--P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42-, and Cl-. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2--N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.

Development and validation of an experimental life support system to study coral reef microbial communities

In the present study, we developed and validated an experimental life support system (ELSS) designed to investigate coral reef associated bacterial communities. The microcosms in the ELSS consisted of coral reef sediment, synthetic seawater, and specimens of five benthic reef species. These included two hard corals Montipora digitata and Montipora capricornis, a soft coral Sarcophyton glaucum, a zoanthid Zoanthus sp., and a sponge Chondrilla sp.. Physicochemical parameters and bacterial communities in the ELSS were similar to those observed at shallow coral reef sites. Sediment bacterial evenness and higher taxonomic composition were more similar to natural-type communities at days 29 and 34 than at day 8 after transfer to the microcosms, suggesting microbial stabilization after an initial recovery period. Biotopes were compositionally distinct but shared a number of ASVs. At day 34, sediment specific ASVs were found in hosts and visa versa. Transplantation significantly altered the bacterial community composition of M. digitata and Chondrilla sp., suggesting microbial adaptation to altered environmental conditions. Altogether, our results support the suitability of the ELSS developed in this study as a model system to investigate coral reef associated bacterial communities using multi-factorial experiments.

Synergetic effects of chlorinated paraffins and microplastics on microbial communities and nitrogen cycling in deep-sea cold seep sediments

Chlorinated paraffins (CPs) and microplastics (MPs) are commonly found in deep-sea cold seep sediments, where nitrogen cycling processes frequently occur. However, little is known about their combined effects on sedimentary microbial communities and nitrogen cycling in these environments. This study aimed to investigate the synergistic impacts of CPs and MPs on microbial communities and nitrogen cycling in deep-sea cold seep sediments through microcosm experiments. Our results demonstrated that the presence of CPs and MPs induced significant alterations in microbial community composition, promoting the growth of Halomonas. Furthermore, CPs and MPs were found to enhance nitrification, denitrification and anammox processes, which was evidenced by the higher abundance of genes associated with nitrification and denitrification, as well as increased activity of denitrification and anammox in the CPs and MPs-treatment groups compared to the control group. Additionally, the enhanced influence of CPs and MPs on denitrification was expected to promote nitrate-dependent and sulfate-dependent anaerobic oxidation of methane, thereby resulting in less methane released into the environment. These findings shed light on the potential consequences of simultaneous exposure to CPs and MPs on biogeochemical nitrogen cycling in deep-sea cold seep sediments.

The dynamic history of prokaryotic phyla: discovery, diversity and division

Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan

BACKGROUND

Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

RESULTS

The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

CONCLUSION

Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality

Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

Aragonite crystallization in a sulfate-rich hypersaline wetland under dry Mediterranean climate (Laguna Honda, eastern Guadalquivir basin, S Spain)

This research investigates the influence of water composition, the presence of seasonal algal mats, detrital inputs and the activity of microorganisms on the crystallization of aragonite in the sediments deposited in the hypersaline Laguna Honda wetland (S of Spain). The high alkaline and hypersaline waters (pH > 9.2 and C.E. > 70 mS/cm) of the wetland lake are rich in SO42- (>24,000 mg/l), Cl- (>21,000 mg/l), Na+ (>11,000 mg/l) Mg2+ (>8400 mg/l) and Ca2+ (>1000 mg/l), and are supersaturated for dolomite, calcite and aragonite. Sediments have lower pH values than column waters, oscillating from 8.54 in the low Eh (up to -80.9 mV) central deep sediments and 6.33 in the shallower higher Eh (around -13.6 mV) shore sediments. Erosion of the surrounding olive groves soils produced detrital silicates rich sediments with concretions of carbonate or sulfate. Aragonite (up to 19 %) and pyrite (up to 13 %) are mainly concentrated in the organic matter rich samples from the upper part of the sediment cores, whereas gypsum is preferably concentrated in low organic matter content samples. Mineral crusts containing a MgAl silicate phase, epsomite, halite and gypsum are precipitated on the floating algal mats covering the wetland waters. Floating algal mats deposit increased the organic matter content of the upper sediments which promoted the presence of fermentative microorganisms, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) communities and variations of Eh that influence the authigenesis of carbonate and S-bearing minerals. Replacement of poorly crystalline MgSi phases infilling algal cells by aragonite was favored in the organic matter rich sediments with low Eh values and important SRB communities that promoted sulfate bioreduction processes to form pyrite. Aragonite precipitation was favored by the increase of carbonate and bicarbonate concentration produced by the SRB oxidation of organic matter, the CO2 degassing by high summer temperatures and the CO2 uptake by photosynthesis of the algal mats.

The function and keystone microbiota in typical habitats under the influence of anthropogenic activities in Baiyangdian Lake

Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake. The results showed that the diversity of microbial community was significantly higher in sediment compared with corresponding water sample. Microbial community showed strong spatial heterogeneity in sediment, and temporal heterogeneity in water. As for different habitats, significantly higher alpha diversity was observed in ecotone, where the interference of human activities was relatively weak. The shared OTUs were distinguished from the keystone taxa, which indicated the uniqueness of microbiota in different ecological habitat. Moreover, the interactions of microbial in ecological restoration area (abandoned fish pond) were relatively simple, suggesting that this ecosystem was relatively fragile compared with others. Based on the metagenomic sequencing, we recognized that the canal, open water, and abandoned fish pond were beneficial for methanogenic and the ecotone might be a hot zone for the oxidation of methane. Notably, most of the microbes that participated in these predominant metabolisms were unclassified, which indicated the hug potential for exploring functional microorganisms in Baiyangdian Lake. This study provided a comprehensive understanding of the ecology characteristics of microbiota in habitats undergoing various human interference in Baiyangdian Lake.

Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas

The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.

Non-mercury methylating microbial taxa are integral to understanding links between mercury methylation and elemental cycles in marine and freshwater sediments

The goal of this study was to explore the role of non-mercury (Hg) methylating taxa in mercury methylation and to identify potential links between elemental cycles and Hg methylation. Statistical approaches were utilized to investigate the microbial community and biochemical functions in relation to methylmercury (MeHg) concentrations in marine and freshwater sediments. Sediments were collected from the methylation zone (top 15 cm) in four Hg-contaminated sites. Both abiotic (e.g., sulfate, sulfide, iron, salinity, total organic matter, etc.) and biotic factors (e.g., hgcA, abundances of methylating and non-methylating taxa) were quantified. Random forest and stepwise regression were performed to assess whether non-methylating taxa were significantly associated with MeHg concentration. Co-occurrence and functional network analyses were constructed to explore associations between taxa by examining microbial community structure, composition, and biochemical functions across sites. Regression analysis showed that approximately 80% of the variability in sediment MeHg concentration was predicted by total mercury concentration, the abundances of Hg methylating taxa, and the abundances of the non-Hg methylating taxa. The co-occurrence networks identified Paludibacteraceae and Syntrophorhabdaceae as keystone non Hg methylating taxa in multiple sites, indicating the potential for syntrophic interactions with Hg methylators. Strong associations were also observed between methanogens and sulfate-reducing bacteria, which were likely symbiotic associations. The functional network results suggested that non-Hg methylating taxa play important roles in sulfur respiration, nitrogen respiration, and the carbon metabolism-related functions methylotrophy, methanotrophy, and chemoheterotrophy. Interestingly, keystone functions varied by site and did not involve carbon- and sulfur-related functions only. Our findings highlight associations between methylating and non-methylating taxa and sulfur, carbon, and nitrogen cycles in sediment methylation zones, with implications for predicting and understanding the impact of climate and land/sea use changes on Hg methylation.

Seasonal and distance-decay patterns of surface sediments microbial nitrogen and sulfur cycling linkage in the eastern coast of China

The surface sediments as a repository of pelagic environment changes and microbial community structural succession tend to have a profound effect on global and local nitrogen and sulfur cycling. In this study, analysis of sediment samples collected from the Bohai Sea, Yellow Sea, and north of the East China Seas (BYnECS) revealed longitude, latitude, depth, and chlorophyll had the strongest influence on microbial community structure (p-values < 0.005). A clear distance-decay pattern was exhibited in BYnECS. The result of co-occurrence network modularization implied that the more active pathway in winter was thiosulfate reduction and nitrate reduction, while in summer it was nitrification. The potential functional genes were predicted in microbial communities, and the most dominant genes were assigned to assimilatory sulfur reduction, denitrification, and dissimilatory nitrate reduction. This study innovatively explored the potential relationships between nitrogen and sulfur cycling genes of these three sea regions in the China Sea.

Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba

Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L-1 MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.

Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea

The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones

BACKGROUND

Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors.

RESULTS

Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones.

CONCLUSIONS

Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract.

Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India

The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.

Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea

IMPORTANCE

Cold seeps occur in continental margins worldwide and are deep-sea oases. Anaerobic oxidation of methane is an important microbial process in the cold seeps and plays an important role in regulating methane content. This study elucidates the diversity and potential activities of major microbial groups in dependent anaerobic methane oxidation and sulfate-dependent anaerobic methane oxidation processes and provides direct evidence for the occurrence of nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) as a previously overlooked microbial methane sink in the hydrate-bearing sediments of the South China Sea. This study provides direct evidence for occurrence of Nr-/N-DAMO as an important methane sink in the deep-sea cold seeps.

Bacterial diversity and community structure of salt pans from Goa, India

In Goa, salt production from the local salt pans is an age-old practice. These salt pans harbor a rich diversity of halophilic microbes with immense biotechnological applications, as they tolerate extremely harsh conditions. Detecting the existence of these microbes by a metabarcoding approach could be a primary step to harness their potential. Three salt pans viz. Agarwado, Curca, and Nerul adjoining prominent estuaries of Goa were selected based on their unique geographical locations. The sediments of these salt pans were examined for their bacterial community and function by 16S rRNA amplicon-sequencing. These salt pans were hypersaline (400-450 PSU) and alkaline (pH 7.6-8.25), with 0.036-0.081 mg/L nitrite, 0.0031-0.016 mg/L nitrate, 6.66-15.81 mg/L sulfate, and 20.8-25.6 mg/L sulfide. The relative abundance revealed that the Pseudomonadota was dominant in salt pans of Nerul (13.9%), Curca (19.6%), and Agarwado (32.4%). The predominant genera in Nerul, Curca, and Agarwado salt pan sediments were Rhodopirellula (1.12%), Sulfurivermis (1.28%), and Psychrobacter (25.5%) respectively. The highest alpha diversity (Shannon-diversity Index) was observed in the Nerul salt pan (4.8) followed by Curca (4.3) and Agarwado (2.03). Beta diversity indicated the highest dissimilarity between Agarwado and the other two salt pans (0.73) viz. Nerul and Curca and the lowest dissimilarity was observed between Nerul and Curca salt pans (0.48). Additionally, in the Agarwado salt pan, 125 unique genera were detected, while in Nerul 119, and in Curca 28 distinct genera were noted. The presence of these exclusive microorganisms in a specific salt pan and its absence in the others indicate that the adjacent estuaries play a critical role in determining salt pan bacterial diversity. Further, the functional prediction of bacterial communities indicated the predominance of stress adaptation genes involved in osmotic balance, membrane modification, and DNA repair mechanisms. This is the first study to report the bacterial community structure and its functional genes in these three salt pans using Next-Generation Sequencing. The data generated could be used as a reference by other researchers across the world for bioprospecting these organisms for novel compounds having biotechnological and biomedical potential.

Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments

Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.

Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland

Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.

Life strategies for Aminicenantia in subseafloor oceanic crust

After decades studying the microbial "deep biosphere" in subseafloor oceanic crust, the growth and life strategies in this anoxic, low energy habitat remain poorly described. Using both single cell genomics and metagenomics, we reveal the life strategies of two distinct lineages of uncultivated Aminicenantia bacteria from the basaltic subseafloor oceanic crust of the eastern flank of the Juan de Fuca Ridge. Both lineages appear adapted to scavenge organic carbon, as each have genetic potential to catabolize amino acids and fatty acids, aligning with previous Aminicenantia reports. Given the organic carbon limitation in this habitat, seawater recharge and necromass may be important carbon sources for heterotrophic microorganisms inhabiting the ocean crust. Both lineages generate ATP via several mechanisms including substrate-level phosphorylation, anaerobic respiration, and electron bifurcation driving an Rnf ion translocation membrane complex. Genomic comparisons suggest these Aminicenantia transfer electrons extracellularly, perhaps to iron or sulfur oxides consistent with mineralogy of this site. One lineage, called JdFR-78, has small genomes that are basal to the Aminicenantia class and potentially use "primordial" siroheme biosynthetic intermediates for heme synthesis, suggesting this lineage retain characteristics of early evolved life. Lineage JdFR-78 contains CRISPR-Cas defenses to evade viruses, while other lineages contain prophage that may help prevent super-infection or no detectable viral defenses. Overall, genomic evidence points to Aminicenantia being well adapted to oceanic crust environments by taking advantage of simple organic molecules and extracellular electron transport.

Ammonia recovery from organic nitrogen in synthetic dairy manure with a microbial fuel cell

Increasing pressures on the animal and cropland agriculture sectors have led to the realization of problems with animal waste management and ammonia-based fertilizer supply. Bioelectrochemical systems (BES) are a new-age technology that offer a way to address these problems. Microbial fuel cells (MFCs), one type of BES, are traditionally used for electricity generation from microbial degradation of organic matters, but can also be used to recover nutrients from wastes simultaneous with treatment. This research investigated an MFC for ammonia recovery from the organic nitrogen (orgN) fraction of synthetic dairy manure, using the simple amino acid glycine as the orgN source. We used five different synthetic manure compositions to determine their effects on MFC performance, and found minimal sacrifices in performance under orgN conditions when compared to the base condition without orgN. The MFC achieved greater than 90% COD removal in all orgN conditions. Nitrogen (N) removal efficiencies of between 40% and 60% were achieved in orgN conditions, indicating that organic nitrogen can be used as the substrate for ammonia mineralization and further recovery as fertilizer. In addition, we found the MFC was largely populated by electrogenic organisms from the phyla Bacteroidota, Firmicutes, Proteobacteria, and Halobacterota, with organisms in both Bacteroidota and Firmicutes capable of N mineralization present. Lastly, we found that in conditions where orgN is scarce and the only N source provided, microbes preferentially degraded organic matter from other dead organisms, especially as an N source. This increases the concentration of N in the MFC system and introduces important operational constraints for MFCs operated for ammonia recovery from orgN.

Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites

Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term “memory of soil”. Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea—among them ammonia-oxidizing and sulphur-related types—are due obviously to former human activities and support the concept of the “ecological memory of soil”.

Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea

Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH₄ dm^-3. Methane carbon isotopic composition (δ¹³C-CH₄) varied from -98.9 to -77.6‱, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4-5.0 nmol dm^-3 day^-1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm^-3 day^-1 at the seep stations. Four lineages of anaerobic methanotrophic archaea (ANME) (1, 2a-2b, 2c, and 3) were found in the deeper sediments at the seep stations along with sulfate-reducing Desulfobacteriota. The ANME-2a-2b clade was predominant among ANME. Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments along with heterotrophic Actinobacteriota and Bacteroidota, and mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae). Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.

Evidence that offshore wind farms might affect marine sediment quality and microbial communities

Offshore wind power is a typical example of clean energy production and plays a critical role in achieving carbon neutrality. Offshore wind farms can have an impact on the marine environment, especially sedimentary environments, but their influence on sediments remain largely unknown. This study, which uses the control-impact principle to define different areas, investigated the characteristics of marine sediments under the Putidao offshore wind farm in Bohai Bay, China. We used chemical and microbiological observations to evaluate sediment quality and microbial community structure. According to both the geo-accumulation index (I_geo) and contamination factor (CF) indexes, copper, chromium and zinc were the major contaminants in the offshore wind farm sediments. The pollution load index (PLI) index showed that the various sites on the wind farm were only lightly polluted compared with baseline values. Closer to the wind farm's center, the metal concentrations started to rise. The physicochemical features of the sediments could better explain changes in the microorganisms present, and screening the microbiomes showed a correlation with heavy metal levels, linking the relative abundance of microorganisms to the sediment quality index. This comprehensive study fills a knowledge gap in China and adds to our understanding of how to assess the sedimentary environments of offshore wind farms.

Bacterial, Archaeal, and Eukaryote Diversity in Planktonic and Sessile Communities Inside an Abandoned and Flooded Iron Mine (Quebec, Canada)

Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities’ diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C1-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown.

Bacterial Communities of Lamiacea L. Medicinal Plants: Structural Features and Rhizosphere Effect

Bacterial communities associated with medicinal plants are an essential part of ecosystems. The rhizosphere effect is rather important in the cultivation process. The purpose of the study was to analyze the rhizosphere effect of oregano (Origanum vulgare L.), peppermint (Mentha piperita L.), thyme (Thymus vulgaris L.), creeping thyme (Thymus serpillum L.) and sage (Salvia officinalis L.). To estimate the quantity of 16S bacteria ribosomal genes, qPCR assays were used. To compare bacterial communities' structure of medicinal plants rhizosphere with bulk soil high-throughput sequencing of the 16S rRNA targeting variable regions V3-V4 of bacteria was carried out. The highest bacterial abundance was associated with T. vulgaris L., M. piperita L. and S. officinalis L., and the lowest was associated with the O. vulgare L. rhizosphere. Phylum Actinobacteriota was predominant in all rhizosphere samples. The maximum bacterial α-diversity was found in S. officinalis L. rhizosphere. According to bacterial β-diversity calculated by the Bray-Curtis metric, T. vulgaris L. root zone significantly differed from bulk soil. The rhizosphere effect was positive to the Myxococcota, Bacteroidota, Verrucomicrobiota, Proteobacteria and Gemmatimonadota.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

Mercury and other trace elements distribution and profiling of microbial community in the surface sediments of East Siberian Sea

In this study, total mercury (THg), methylmercury (MeHg), various trace elements, and microbial communities were measured in surface sediments of the East Siberian Sea (ESS). The results showed that the average values of THg and MeHg were 58.8 ± 15.21 μg/kg and 0.50 ± 0.22 μg/kg, respectively. The notable levels of trace elements present in both surface sediment and porewater were Al, Fe, and Mn. The enrichment factor and geoaccumulation index analyses found that both natural phenomena and anthropogenic activities contributed to elevated concentrations of metals in the ESS. The redox proxy metals, pH, and SO₄^2- were the major factors influencing the THg and MeHg distributions. Microbial profiles were substantially affected by metals and other abiotic factors. Proteobacteria and Thaumarchaeota were the most abundant phyla. Overall, the findings presented here facilitate the understanding of the current status of metal contamination, its influencing factors, and metal-microbiota-interactions in ESS.

Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters

In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.