Sediment Microbial Communities Research Articles

Sediment carbon storage in subtidal beds of the invasive seagrass Halophila stipulacea along an extreme water depth gradient, St. Thomas, U.S. Virgin Islands

Blue carbon ecosystems such as mangroves, salt marshes, and seagrass beds are found globally and are fundamental to fisheries production, storm surge protection, and carbon sequestration. The contribution of seagrass ecosystems to global carbon stocks is still not well understood, including in the United States Virgin Islands (USVI). No study has been published to-date assessing the sediment carbon density (SCD) in seagrass beds in the USVI. This study focused on the carbon storage ability of the invasive species, Halophila stipulacea, which is compact in size compared to common native seagrasses and has spread rapidly to become a dominant seagrass in the USVI. This species forms dense mats across a wide depth range (<1m to 50m) typically uninhabitable to its native counterparts (Syringodium filiforme and Thalassia testudinum). Several biotic and abiotic factors influence the carbon storage ability of seagrass, yet little is known about carbon storage sequestration along a depth gradient for H. stipulacea. This study provides the first assessment of the biological characteristics (shoot density, leaf area, leaf height, and percent cover) and carbon storage ability of H. stipulacea across a depth gradient (shallow: 5-10m; medium: 15-20m; deep: 25-30m) at two sites in St. Thomas, USVI. Mean sediment carbon density (SCD) values per core reported for H. stipulacea in this study ranged from 3.88 to 15.67mgC/cm3; these were comparable to regional and global seagrass studies. Biological characteristics were not an accurate predictor of SCD. A significant interaction between water depth and site was found to affect mean SCD of H. stipulacea beds. It is likely that site-specific factors most likely account for variations seen within the data. Although carbon values in this study compared to values reported in the literature, other factors such as land use, proximity to carbon sources, sediment microbial community, and water current patterns may be driving SCD values. These findings highlight the need for site and species-specific carbon storage assessments on local to regional scales to accurately estimate current and forecasted blue carbon stocks.

Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments.

The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.

Response of sediment microbial communities to the flow effect of the Triangular Artificial Reef: A simulation-based experimental study

Artificial reefs (ARs), as an important tool for habitat restoration, play significant impacts on benthic microbial ecosystems. This study utilized 16S rRNA gene sequencing technology and computational fluid dynamics (CFD) flow simulation to investigate the effects of flow field distribution around ARs on microbial community structure. The results revealed distinct regional distribution patterns of microbial communities affected by different hydrodynamic conditions. Flow velocity and flow regime of water in sediment-water interface shaped the microbial community structure. The diversity and richness in R-HF were significantly decreased compared to other five regions (p<0.05). At the phyla and OUT levels, most abundant taxa (1>%) showed an enrichment trend in R-HB. However, more than half of differentially abundant taxa were enriched in R-HB, which was significantly correlated with organic matter (OM). Bugbase phenotypic predictions indicated a low abundance of the anaerobic phenotype in R-HF and a high abundance of the biofilm-forming phenotype in R-HB.

Control of phosphorus release from sediment by iron/aluminum co-modified zeolite: efficiency, mechanism, and response of microbial communities in sediment.

The efficiency of iron/aluminum co-modified zeolite (FeAl-Z) covering and amendment for controlling the internal loading of phosphorus (P) from sediment to the overlying water (OW) and its controlling mechanism were explored. The response of the composition of sedimentary microbial communities in sediment and their function to the FeAl-Z capping and amendment was also examined. FeAl-Z showed good removal performance for phosphate in aqueous solution. The maximum phosphate adsorption quantity for FeAl-Z at pH 7 attained 11.2mg P/g. The release of sediment endogenous phosphorus to OW can be successfully restrained by the FeAl-Z covering and amendment, and the suppression ability of FeAl-Z covering was stronger than that of FeAl-Z amendment. Under the capping or amendment condition, FeAl-Z can effectively inactivate the labile phosphorus measured by diffusion gradient in thin film (DGT-LP) in the overlying water and surface sediment. The added FeAl-Z transformed redox-sensitive phosphorus (BD-P) to metal oxide-bound phosphorus (NaOH-IP) and residual phosphorus (Res-P) in sediment, which increased the stability of inorganic phosphorus in the sediment. The passivation of soluble reactive phosphorus (SRP) and DGT-LP in the surface sediment by FeAl-Z significantly contributed to the inhibition of sediment endogenous phosphorus release to OW by the FeAl-Z capping, and the passivation of SRP, DGT-LP and mobile phosphorus in the surface sediment played a pivotal role in the control of sediment internal phosphorus release by the FeAl-Z amendment. The FeAl-Z amendment and capping did not increase the liberation risk of Fe from sediment, and the microorganisms in the sediments under the conditions of FeAl-Z amendment and covering still can perform good ecological functions. Results of this research demonstrate that FeAl-Z capping has high application potential in the control of phosphorus transfer from sediment to OW.

Cyanobacterial bloom affects structural and functional succession of microbial communities in urban wetland sediments in the Qinghai Plateau

Abstract Algal blooms significantly affect microbial community in wetland ecosystems. However, little is known about the succession of sediment microbial community during algal blooms. This study aimed to investigate the temporal patterns of sediment bacterial community structure and function succession during algal blooms (March to May, 2022) with high-throughput sequencing technology. To this end, algal blooms were divided into the bloom stage (BS), decomposition stage (DS) and end stage (ES). The results showed that: (1) The algal blooms were dominated by Microcystis species within Cyanobacteria. Both phytoplankton abundance and biomass reached the peak in the BS, with 45.78×105 cells/L and 5.97 mg/L, respectively. (2) The alpha diversity indices of sediment bacterial community showed a monotonically increasing trend, with the lowest value in the BS. Cyanobacterial blooms reduced the relative abundance of Actinobacteria and Chloroflexi, and raised that of Firmicutes, Proteobacteria and Bacteroidetes. (3) Cyanobacterial blooms remarkably decreased the complexity of the co-occurrence network of the sediment bacterial community, which resisted extreme environmental conditions in the BS and DS by increasing positive relationships. (4) Mantel test showed that phytoplankton biomass, T, DO, and OC had significant effects on the sediment bacterial community. The results of this study are important for the ecological management of algal blooms through microorganisms.

Added Biochars Promoted Nitrogen and Phosphorus Removal from Ecological Ditches at Low Temperature

The global issue of ecological ditches being poor in removing nitrogen and phosphorus under cold winter temperatures has been identified. This study introduced three types of biochar (reed, rice, and corn) into ecological ditch sediments via two application methods: rhizosphere and mixed addition. The purpose was to explore how these methods affect the removal of nitrogen and phosphorus, as well as their influences on microbial communities in sediments. The results indicated that the addition of biochar to ecological ditches significantly enhanced the removal of nitrogen and phosphorus. Among the three types of biochar, the mixed addition of corn biochar yielded the greatest results, achieving removal rates of 77.1% for total nitrogen (TN), 93.3% for NH4+-N, and 90.3% for total phosphorus (TP). The growth of Vallisneria natans was greatly improved by the mixed addition method, resulting in an average increase of 154%. This improvement was superior to the rhizosphere addition group, which led to a growth increase of 125%. In comparison, the control group (CK) showed a decrease of 4.8% in growth. Different methods of biochar addition resulted in changes in the physicochemical properties and stoichiometry of the plants. Microbial analyses showed that the addition of biochar reduced the diversity and abundance of the substrate microbial community.

Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities.

o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.

Relationships between high-concentration toxic metals in sediment and evolution of microbial community structure and carbon-nitrogen metabolism functions under long-term stress perspective.

Microorganisms are highly sensitive to toxic metal pollution and play an important role in the material cycling and energy flow of the water ecosystem. Herein, 13 sediment samples from Junchong Reservoir (Guangxi Province, China) were collected in December 2021. The spatial distribution of pollution levels for toxic metals and the effects of toxic metals on the composition, functional characteristics, and metabolism of microorganisms were investigated. The results demonstrated that the area is a proximate area to industrial zones with severity of toxic metal pollution. Their mean concentrations of As, Cu, Zn, and Pb were up to 128.79mg/kg, 57.62mg/kg, 594.77mg/kg, and 97.12mg/kg respectively. There was a strong correlation between As, Cu, Zn, and Pb, with the highest correlation coefficient reaching 0.94. As the level of toxic metal pollution increases, the diversity and abundance of microorganisms gradually decrease. Compared to those with lower pollution levels, the Shannon index in regions with higher pollution levels decreases by up to 0.373, and the Chao index decreases by up to 143.507. However, the relative abundance of Bacteroidota, Patescibacteria, and Chloroflexi increased by 23%, 20%, and 5%, respectively, indicating their higher adaptability to toxic metals. Furthermore, microbial carbon and nitrogen metabolism were also affected by the presence of toxic metals. FAPROTAX analysis demonstrated an abundant reduction of ecologically functional groups associated with carbon and nitrogen transformations under high toxic metal pollution levels. KEGG pathway analysis indicated that carbon fixation and nitrogen metabolism pathways were inhibited with increasing toxic metal concentrations. These findings would contribute to a better understanding of the effects of toxic metal pollution on sediment microbial communities and function, shedding light on the ecological consequences of toxic metal contamination.

Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.

Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs)and 55 secondary metabolites (SMs)within 35 high-quality metagenome-assembled genomes (MAGs)derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.

Impacts of oxbow lake evolution on sediment microbial community structure in the Yellow River source region

Oxbow lake formation and evolution have significant impacts on the fragile Yellow River Basin ecosystem. However, the effects of different oxbow lake evolutionary stages on sediment microbial community structure are not yet understood comprehensively. Therefore, microbial community structure in three stages of oxbow lake succession, namely, lotic lake (early stage), semi-lotic lake (middle stage), and lentic lake (late stage), was investigated in the present study in the Yellow River Basin on the Qinghai-Tibet Plateau. Amplicon sequencing was employed to reveal differences in microbial community diversity and composition. The bacterial and fungal communities in sediment were significantly different among the three succession stages and were driven by different environmental factors. In particular, bacterial community structure was influenced primarily by nitrate-nitrogen (N), microbial biomass phosphorus, and total carbon (C) and organic C in the early, middle, and late stages, respectively. Conversely, fungal community structure was influenced primarily by ammonium-N in the early stage and by moisture content in the middle and late stages. However, the predicted functions of the microbial communities did not exhibit significant differences across the three succession stages. Both bacteria and fungi were influenced significantly by stochastic factors. Homogeneous selection had a high relative contribution to bacteria community assembly in the middle stage, whereas the relative contributions of heterogeneous selection processes to fungal community assembly increased through the three stages. As succession time increased, the total number of keystone species increased gradually, and the late succession stage had high network complexity and the highest network stability. The findings could facilitate further elucidation of the evolution mechanisms of oxbow lake source area, high-altitude river evolution dynamics, in addition to aiding a deeper understanding of the long-term ecological evolution patterns of source river ecosystems.

Unveiling the impact of microplastics with distinct polymer types and concentrations on tidal sediment microbiome and nitrogen cycling

Microplastics (MPs) are distributed widely in the ocean surface waters and sediments. Increasing MPs contamination in intertidal zone profoundly impacts microbial ecosystem services and biogeochemical process. Little is known about the response of tidal sediment microbiome to MPs. We conducted a 30-day laboratory microcosm study using five polymers (PE, PBS, PC, PLA and PET) at three concentrations (1%, 2% and 5%, w/w). High throughput sequencing of 16S rRNA, qPCR and enzyme activity test were applied to demonstrate the response of microbial community and nitrogen cycling functional genes to MPs. MPs reduced the microbial alpha diversity and the microbial dissimilarity while the effects of PLA-MPs were concentration dependent. LEfSe analysis indicated that the Proteobacteria predominated for all MP treatments. Mantel’s test, RDA and correlation analysis implied that pH may be the key environmental factor for causing microbial alterations. MPs enhanced nitrogen fixation in tidal sediment. PLA levels of 1% but not 5% produced the most significant effects in nitrogen cycling functional microbiota and genes. PLS-PM revealed that impacts of MPs on tidal sediment microbial communities and nitrogen cycling were dominated by indirect effects. Our study deepened understanding and filled the knowledge gap of MP contaminants affecting tidal sediment microbial nitrogen cycling. Environment implicationThe global prevalence of plastic waste has resulted in the severely continuous accumulation of MPs especially in tidal sediments. Compared to MPs exposure on soil or absolute sediment, the exposure of MPs with different polymers and concentrations affected the nitrogen cycling in the tidal sediment, enhancing nitrogen fixation while indicating non-consistent effects on the other processes. The present work clarified the toxicological effects of MPs on tidal sediment, filling the knowledge gap about how MPs affected microbial nitrogen cycling in intertidal zone.

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.

Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland.

Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.

Adsorption, natural attenuation, and microbial community response of ofloxacin and oxolinic acid in marine sediments

The pollution of quinolone antibiotics in the marine environment has attracted widespread attention, especially for ofloxacin (OFL) and oxolinic acid (OXO) due to their frequent detection. However, few studies have been conducted to assess the behaviors and microbial community response to these antibiotics in marine sediments, particularly for potential antibiotic-resistant bacteria. In this work, the adsorption characteristics, natural attenuation characteristics, and variation of microbial communities of OFL and OXO in marine sediments were investigated. The adsorption process of antibiotics in sediments occurred on the surface and internal pores of organic matter, where OFL was more likely to be transferred from seawater to sediment compared with OXO. Besides, the adsorption of two antibiotics on sediment surfaces was attributed to physisorption (pore filling, electrostatic interaction) and chemisorption (hydrogen bonding). The natural attenuation of OFL and OXO in marine sediment followed second-order reaction kinetics with half-lives of 6.02 and 26.71 days, respectively, wherein biodegradation contributed the most to attenuation, followed by photolysis. Microbial community structure in marine sediments exposure to antibiotics varied by reducing abundance and diversity of microbial communities, as a whole displaying as an increase in the relative abundance of Firmicutes whereas a decrease of Proteobacteria. In detail, Escherichia-Shigella sp., Blautia sp., Bifidobacterium sp., and Bacillus sp. were those antibiotic-resistant bacteria with potential ability to degrade OFL, while Bacillus sp. may be resistant to OXO. Furthermore, functional predictions indicated that the microbial communities in sediment may resist the stress caused by OFL and OXO through cyano-amino acid metabolism, and ascorbate and aldarate metabolism, respectively. The research is key to understanding fate and bacterial resistance of antibiotics in marine sediments.

Arsenic-methylating microbial community in sediment along the water flow is correlated with the distance to a low-temperature hot spring

Abstract Microbially mediated arsenic methylation, remains understudied in subgeothermal environments. This study aimed to investigate the activity and diversity of arsM-carrying microorganisms in sediment samples (termed YC1, YC2, and YC5) from a low-temperature hot spring. Microcosm assays revealed that only YC1 and YC2 exhibited limited As-methylating activities, generating a maximum of 2.3–3.5 μg/L methylarsenate (MMA) and 2.2–2.8 μg/L dimethylarsenate (DMA). The addition of lactate and arsenite significantly promoted these activities, increasing the concentrations to 26.1–184.0 μg/L MMA and 38.1–204.0 μg/L DMA. The arsM gene abundance also increased by 46–276%, indicating that lactate can activate arsenite methylation. YC1 and YC2, which were closer to the hot spring hole than YC5 was, had similar patterns, and shared a similar arsM community structure, dominated by Actinobacteriota, Firmicutes, and Proteobacteriota on days 7 and 21. In contrast, at YC5, the sampling site far from the spring hole, representatives of Acidobacteriota were dominant on day 7, whereas those of Actinobacteriota were prevalent on day 21. Acidobacteriota co-occurred with dimethylarsenate production, and Mycobacterium co-occurred with DMA demethylation. These findings suggested that the low-temperature arsenic hot spring possessed diverse arsenic-methylating species, whereas demethylating bacteria preferred to inhabit niches farther from the hot spring.

Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes.

Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes-like dispersal limitation-contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.

Microplastics strengthen nitrogen retention by intensifying nitrogen limitation in mangrove ecosystem sediments

Mangrove wetlands are hotspots of the global nitrogen (N) cycle and important sinks of microplastics (MPs) due to their ecotone location between terrestrial and marine ecosystems. However, the effects of MPs on N cycle processes in mangrove ecosystems are still poorly understood. Thus, the present study assessed the impacts by adding MPs to mangrove sediments in a microcosm incubation experiment. The results showed that MPs increased dissolved organic carbon and nitrate but reduced ammonium contents in the sediments. MPs increased C:N stoichiometric and N:C-acquiring enzymatic ratios, indicating an intensified N limitation in mangrove sediments following exposure of MPs. MPs decreased microbial community diversity and shifted sediment microbial communities from r- to K-strategists, consistent with the intensified N limitation. In response, dissimilatory nitrate reduction to ammonium (DNRA) rates increased while nitrous oxide (N2O) production reduced suggesting more efficient N utilization in MPs treatments. The MPs with heteroatoms such as PLA- and PVC-MPs, increased DNRA rates by 67.5–78.7%, exhibiting a stronger impact than PE-MPs. The variation partitioning analysis revealed that the variances of DNRA rates and N2O production could be attributed to synergistic effects of physicochemical properties, nutrient limitation, and microbial community in mangrove sediments. Overall, this study provides pertinent insights into the impacts of MPs as a new carbon source on nutrient limitation and N turnover in mangrove ecosystems.

Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis

ABSTRACT The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.

Growth Performance and Environmental Quality Indices and Biomarkers in a Co-Culture of the European Sea Bass with Filter and Deposit Feeders: A Case Study of an IMTA System

This study aimed to evaluate the efficiency of an integrated multi-trophic aquaculture (IMTA) system comprising co-cultured fed fish and organic extractive species representing three distinct trophic levels as well as the impact and potential utilization of two commercially available fish feeds made up of 35% fish meal (FM) and 20% fish meal (LFM) ingredients, using a multi-indicator assessment approach. Significant alterations were observed in growth performance indicators (GPIs), water and sediment quality indices, toxicity tests and biomarkers within the IMTA system. The fish survival, weight gain (WG), and specific growth rate (SGR) were higher in the IMTA system with significantly lower feed conversion ratios (FCRs) and higher feed efficiency (FE) in comparison to the fed fish monoculture system. Yet, organic filter feeders displayed 100% survival, and increased shell growth, while deposit feeders exhibited successful survival and significant weight gain. In the comparison between FM-IMTA and LFM-IMTA, fed fish in FM-IMTA showed higher WG, SGR, and FE with lower FCR. Environmental parameters like temperature, oxygen, and nutrient concentrations fluctuated but generally improved in the IMTA system, indicating lower mesotrophic conditions. Sediment fatty acid profiles differed between systems and toxicity assessments, which suggested a lower impact in IMTA and FM-IMTA systems. The sediment microbial community displayed high similarity within IMTA systems and between FM-IMTA and LFM-IMTA. These findings underscore the potential of IMTA systems for sustainable aquaculture, emphasizing improved growth performance and reduced environmental impact, particularly when using fish meal feeds.

Temporal profiling of sediment microbial communities in the Three Gorges Reservoir Area discovered time-dissimilarity patterns and multiple stable states

Microbial communities play vital roles in cycling nutrients and maintaining water quality in aquatic ecosystems. To better understand the dynamics of microbial communities and to pave way to effective ecological remediation, it's essential to reveal the temporal patterns of the communities and to identify their states. However, research exploring the dynamic changes of microbial communities needs a large amount of time-series data, which could be an extravagant requirement for a single study. In this research, we overcame this challenge by conducting a meta-analysis of years of accumulations of 16S rRNA high-throughput sequencing data from the Three Gorges Reservoir Area (TGRA), an ecological and environmental hotspot. For better understanding the microbial communities time-dissimilarity dynamics, three microbial communities time-dissimilarity patterns were hypothesized, and the linear pattern in the TGRA was validated. In addition, to explore the stability of microbial communities in the TGRA, two alternative stable states were revealed, and their differences in community richness, alpha diversity indices, community composition, ecological network topological properties, and metabolic functions were demonstrated. In short, two states of microbial communities showed distinct richness and alpha diversity indices, and the communities in one state were more dominated by Halomonas and Nitrosopumilaceae genera, facilitating nitrogen cycling metabolic processes; whilst the main genera of the other state were Bathyarchaeia and Methanosaeta, which favored methane-related metabolism. Moreover, different studies and environmental differences between mainstream and tributaries were attributed as the potential inducing factors of the state division. Our study provides a comprehensive insight into the dynamics and stability of microbial communities in the TGRA, and a reference for future studies on microbial community dynamics.