Sediment Microbial Communities Research Articles

Impacts and mechanism of biodegradable microplastics on lake sediment properties, bacterial dynamics, and greenhouse gasses emissions

The accumulation of microplastics (MPs) in freshwater ecosystems plays a vital role in greenhouse gases (GHGs) emissions from lake sediment by altering sediment properties and microbial communities. Thus, a short-term microcosm experiment was performed to explore the effect of conventional polyethylene (PE) and biodegradable Poly (butylene-adipate-co-terephtalate) (PBAT) MPs on carbon dioxide (CO2) and methane (CH4) emissions from lake sediment and associated microbial community. The results indicated that at 1.0 % concentration, the cumulative CO2 emissions were increased by 16.8 % and the cumulative CH4 emissions were increased more than four times following the addition of biodegradable MPs compared to conventional MPs, which was due to the more dissolved organic carbon (DOC) provided by biodegradable MPs for microbial respiration. Furthermore, the cumulative CO2 and CH4 emissions significantly (p < 0.05) increased with the increasing concentrations of biodegradable MPs. Notably, the accumulation of MPs could weaken the microbial stress from requirements of energy and substrate, and increase the microbial biomass carbon (MBC) value, thus eventually improving the respiratory capacity of microbes. In addition, the biodegradable MPs significantly increased the abundance of microbes, such as Firmicutes, Myxococcota and Actinobacteriota, which were related to the function of anaerobic respiration. Overall, we concluded that the abundant DOC provided by biodegradable MPs could promote the growth of microbes in lake sediment, and they could change the structure and diversity of the microbial community, which would eventually enhance the anaerobic respiration of microbes and aggravate the GHGs emissions.

Climatic effect from oyster reef restoration in Spartina alterniflora invaded intertidal mudflat: From the perspective of CH4 and N2O production

Spartina alterniflora is a dominant invasive species along the coast of China. A surprising phenomenon that the oyster reef formation is substituting the S. alterniflora invasion, was recently observed in the west coast of Bohai Bay, North China. As the intertidal mudflat ecosystem is critical for coastal blue carbon, this paper aims to evaluate the climatic effect of the alternation from the perspective of potential CH4 and N2O production. The sediment geochemical properties and potential CH4 and N2O productions were therefore measured in sediments dominated by Spartina alterniflora (SA), oyster reef (OR), mixture of S. alterniflora and oyster reef (SA-OR) and bare mudflat (BM) at an intertidal mudflat. Meanwhile, sediment microbial community structure and function genes were also determined utilizing metagenome high-throughput sequencing technology. Our results indicated that the formation of oyster reef in S. alterniflora invaded intertidal mudflat might slightly reduce the sediment potential CH4 production and enhance the sediment potential N2O production. The oyster reef formation could alter the community composition of methanogens and the abundance of functional genes in methanogenesis, and transform the main pathway from methylotrophic to hydrogenotrophic methanogenesis in surface sediments. Metagenome sequencing revealed that the oyster reef formation may promote nitrification, inhibit dissimilatory nitrate reduction (DNRA) and nitrate assimilation functions, and reduce the abundance of nosZ genes. Mantel analysis showed that pH, soluble salt and dissolved carbon (DC) were the most important factors influencing the composition of microbial community. In general, our results imply that the growth of oyster reef in the S. alterniflora invaded area has opposing effects from the prospective of the potential CH4 and N2O production.

Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds

BackgroundIn New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation.ResultsDrying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture.ConclusionThe efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.

Site-specific response of sediment microbial community to supplementation of polyhydroxyalkanoates as biostimulants for PCB reductive dechlorination

The use of biodegradable plastics is constantly raising, increasing the likeliness for these polymers to end up in the environment. Environmental applications foreseeing the intentional release of biodegradable plastics have been also recently proposed, e.g., for polyhydroxyalkanoates (PHAs) acting as slow hydrogen releasing compounds to stimulate microbial reductive dehalogenation processes. However, the effects of their release into the environment on the ecosystems still need to be thoroughly explored. In this work, the use of PHAs to enhance the microbial reductive dechlorination of polychlorobiphenyls (PCBs) and their impact on the metabolic and compositional features of the resident microbial community have been investigated in laboratory microcosms of a polluted marine sediment from Mar Piccolo (Taranto, Italy), and compared with recent findings on a different contaminated marine sediment from Pialassa della Baiona (Ravenna, Italy). A decreased biostimulation efficiency of PHAs on PCBs reductive dechlorination was observed in the sediment from Mar Piccolo, with respect to the sediment from Pialassa della Baiona, suggesting that the sediments' physical-chemical characteristics and/or the biodiversity and composition of its microbial community might play a key role in determining the outcome of this biostimulation strategy. Regardless of the sediment origin, PHAs were found to have a specific and pervasive effect on the sediment microbial community, reducing its biodiversity, defining a newly arranged microbial core of primary degraders and consequently affecting, in a site-specific way, the abundance of subdominant bacteria, possibly cross-feeders. Such potential to dramatically change the structure of autochthonous microbial communities should be carefully considered, since it might have secondary effects, e.g., on the natural biogeochemical cycles.

Bacterial Community Diversity in Channel Sediments of Different Disturbance Sections of the Jialing River

In order to explore the impact of different anthropogenic disturbances on the ecological environment of natural rivers, the bacterial community in the channel sediments of the Jialing River was taken as the research object, and the high-throughput sequencing technique was used to analyze the community composition and functional changes of bacteria in the channel sediments of rivers with engineering disturbance, tributary disturbance, sand mining disturbance, reclamation disturbance, and undisturbed section. The results showed that there were significant differences in the physical and chemical properties of channel sediments and bacterial community diversity in different disturbance sections of the Jialing River (P<0.05). The undisturbed section had the highest bacterial community diversity, whereas the sand mining disturbance and undisturbed section had the highest bacterial community uniformity, and tributary disturbance and reclamation disturbance both resulted in a decrease in bacterial community diversity and uniformity. The effect of engineering disturbance on bacterial community composition was significantly different from that of the other four disturbance sections. The dominant bacterial phyla were Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi, and the dominant bacterial classes were γ-Proteobacteria, α-Proteobacteria, and Vicinamibacteria. Sand mining disturbance led to the increase in Actinobacteria, and engineering disturbance promoted the increase in Acidobacteria. Moisture content, total organic carbon, total nitrogen, and total phosphorus were the main environmental factors affecting the changes in sediment microbial communities. The bacterial communities mainly involved four categories of primary metabolic functions, including metabolism, genetic information processing, environmental information processing, and cellular processes, and 18 categories of secondary metabolic functions, such as global and overview maps, carbohydrate metabolism, amino acid metabolism, cofactor and vitamin metabolism, and energy metabolism. Human interference led to significant changes in energy metabolism, cofactor and vitamin metabolism, nucleotide metabolism, replication and repair, and translation (P<0.05). In conclusion, anthropogenic disturbance led to the mutation of bacterial community diversity and function, which destroyed the stability of the microbial community structure in Jialing River sediments.

Responses of the structure and function of microbes in Yellow River Estuary sediments to different levels of mercury

The health and stability of the estuary of the Yellow River ecosystem have come under increasing pressure from land-based inputs of heavy metals. While it is known that heavy metals affect the function and health of the microbial community, there remains little knowledge on the responses of the microbial community to heavy metals, particularly highly toxic mercury. The research aimed to characterize the responses of the sediment microbial community of the estuary of the Yellow River to different levels of mercury stress. Estuary sediment samples were collected for microbial community analysis, measurement of mercury [including total mercury (THg) and methylmercury (MeHg)], and measurement of other physicochemical factors, including pH, total organic carbon (TOC), sulfide, iron ratio (Fe3+/Fe2+), ammonium salt (NH4+), and biochemical oxygen demand (BOD). The application of 16S rRNA sequencing identified 60 phyla of bacteria, dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stations with higher THg or MeHg and lower microbial abundance and diversity were generally distributed further outside of the estuary. Besides mercury, the measured physicochemical factors had impacts on microbial diversities and distribution. Metagenomics assessment of three stations, representative of low, moderate, and high mercury concentrations and measured physicochemical factors, revealed the abundances and functions of predicted genes. The most abundant genes regulating the metabolic pathways were categorized as metabolic, environmental information processing, and genetic information processing, genes. At stations with high levels of mercury, the dominant genes were related to energy metabolism, signal transport, and membrane transport. Functional genes with a mercury-resistance function were generally in the mer system (merA, merC, merT, merR), alkylmercury lyase, and metal-transporting ATPase. These results offer insight into the microbial community structure of the sediments in the Yellow River Estuary and the microbial function of mercury resistance under mercury stress.

Toxicity evaluation of a heavy-metal-polluted river: Pollution identification and bacterial community assessment.

The Salt River is an important urban river in Kaohsiung, Taiwan. In this study, the source identification and risk and toxicity assessment of the heavy-metal-contaminated sediments in the Salt River were investigated. The geo-accumulation index (Igeo), enrichment factor (EF), sediment quality guidelines (SQGs), potential ecological risk index (RI), pollution load index (PLI), and toxic units (TU) were applied to determine effects of heavy metals on microbial diversities and ecosystems. Results from the ecological and environmental risk assessment show that high concentrations of Zn, Cr, and Ni were detected in the midstream area and the sum of toxic units (ΣTUs) in the midstream (7.2-32.0) is higher than in the downstream (14.0-19.7) and upstream (9.2-17.1). It could be because of the continuous inputs of heavy-metal-contained wastewaters from adjacent industrial parks. Results also inferred that the detected heavy metals in the upstream residential and commercial areas were possibly caused by nearby vehicle emissions, non-point source pollution, and domestic wastewater discharges. Results of metagenomic assays show that the sediments contained significant microbial diversities. Metal-tolerant bacterial phyla (Proteobacteria: 24.4%-46.4%, Bacteroidetes: 1.3%-14.8%, and Actinobacteria: 2.3%-11.1%) and pathogenic bacterial phyla (Chlamydiae: 0.5%-37.6% and Chloroflexi: 5.8%-7.2%) with relatively high abundance were detected. Metal-tolerant bacteria would adsorb metals and cause the increased metal concentrations in sediments. Results indicate that the bacterial composition in sediment environments was affected by anthropogenic pollution and human activities and the heavy-metal-polluted ecosystem caused the variations in bacterial communities. PRACTITIONER POINTS: Microbial community in sediments is highly affected by heavy metal pollution. Wastewaters and vehicle traffic contribute to river sediments pollution by heavy metals. Proteobacteria, Bacteroidota, and Actinobacteria are dominant heavy-metal-tolerant bacterial phyla in sediments. Toxicity assessment is required to study risk levels of heavy-metal contained sediments.

Long-term biodegradation of crude oil in high-arctic backshore sediments: The Baffin Island Oil Spill (BIOS) after nearly four decades

With an on-going disproportional warming of the Arctic Ocean and the reduction of the sea ice cover, the risk of an accidental oil spill from ships or future oil exploration is increasing. It is hence important to know how crude oil weathers in this environment and what factors affect oil biodegradation in the Arctic. However, this topic is currently poorly studied. In the 1980s, the Baffin Island Oil Spill (BIOS) project carried out a series of simulated oil spills in the backshore zone of beaches located on Baffin Island in the Canadian High Arctic. In this study two BIOS sites were re-visited, offering the unique opportunity to study the long-term weathering of crude oil under Arctic conditions. Here we show that residual oil remains present at these sites even after almost four decades since the original oiling. Oil at both BIOS sites appears to have attenuated very slowly with estimated loss rates of 1.8–2.7% per year. The presence of residual oil continues to significantly affect sediment microbial communities at the sites as manifested by a significantly decreased diversity, differences in the abundance of microorganisms and an enrichment of putative oil-degrading bacteria in oiled sediments. Reconstructed genomes of putative oil degraders suggest that only a subset is specifically adapted for growth under psychrothermic conditions, further reducing the time for biodegradation during the already short Arctic summers. Altogether, this study shows that crude oil spilled in the Arctic can persist and significantly affect the Arctic ecosystem for a long time, in the order of several decades.

Effects of different chemical agents on changes in sediment phosphorus composition and the response of sediment microbial community

Controlling the release of sediment phosphorus (P) using chemical agents is a promising method for controlling internal P in eutrophic lakes. However, mineral P formation and changes in the organic P composition after sediment amendment with P-inactivation agents remain poorly understood. Furthermore, little is known about the changes in the sediment microbial community composition after remediation. Here, various ratios of poly aluminum chloride (PAC) and lanthanum-modified bentonite (LMB) were added to nutrient-rich sediments and incubated. Sequential P extraction, solution/solid-state 31P nuclear magnetic resonance (NMR), and microbial analyses were periodically performed on the inactivated sediments. The results indicate that PAC and LMB effectively reduced sediment iron-bound P and organic P, respectively, markedly increasing the content of aluminum- and calcium-bound P in the sediment, respectively. Solid-state 31P NMR results confirmed the formation of rhabdophane (LaPO4. nH2O) in the LMB-amended sediment. Solution 31P NMR results showed that PAC preferentially reduced the organic P fractions of pyrophosphate, whereas LMB efficiently reduced the organic P fractions of orthophosphate, monoesters, and diesters in the sediment. Compared with the control sediment, PAC addition can cause short-term negative effects on sediment microbes at high doses, whereas LMB addition can increase bacterial diversity or richness in the sediment. These results provide a deeper understanding of the differences between PAC and LMB in internal sediment P control.

Laboratory tidal microcosm deciphers responses of sediment archaeal and bacterial communities to microplastic exposure

Microplastics (MPs) are 1–5 mm plastic particles that are serious global contaminants distributed throughout marine ecosystems. However, their impact on intertidal sediment microbial communities is poorly understood. In this study, we conducted a 30-day laboratory tidal microcosm experiment to investigate the effects of MPs on microbial communities. Specifically, we used the biodegradable polymers polylactic acid (PLA) and polybutylene succinate (PBS), as well as the conventional polymers polyethylene terephthalate (PET), polycarbonate (PC), and polyethylene (PE). Treatments with different concentrations (1–5%, w/w) of PLA- and PE-MPs were also included. We analyzed taxonomic variations in archaeal and bacterial communities using 16S rRNA high-throughput sequencing. PLA-MPs at concentrations of 1% (w/w) rapidly altered microbiome composition. Total organic carbon and nitrite nitrogen were the key physicochemical factors and urease was the major enzyme shaping MP-exposed sediment microbial communities. Stochastic processes predominated in microbial assembly and the addition of biodegradable MPs enhanced the contribution of ecological selections. The major keystone taxa of archaea and bacteria were Nitrososphaeria and Alphaproteobacteria, respectively. MPs exposure had less effect on archaeal functions while nitrogen cycling decreased in PLA-MPs treatments. These findings expanded the current understanding of the mechanism and pattern that MPs affect sediment microbial communities.

Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities.

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.

The response mechanism of microorganisms to the organic carbon-driven formation of black and odorous water

The formation of black and odorous water is a complex process influenced by various factors such as organic matter and environmental conditions. However, there are limited studies on the role of microorganisms in water and sediment during the blackening and odorization process. In this study, we investigated the characteristics of black and odorous water formation by simulating organic carbon-driven black and odorous water through indoor experiments. The study revealed that the water turned black and odorous when DOC reached 50 mg/L and the microbial community structure in the water changed significantly during this process, with the relative abundance of Desulfobacterota increasing significantly and Desulfovibrio being the main dominant genus in Desulfobacterota. Additionally, we observed a notable decrease in the α-diversity of the microbial community in water and a considerable increase in microbial function of sulfur compounds respiration in water. In contrast, the sediment microbial community changed slightly, and the main functions of the sediment microbial community remained unchanged. The partial least squares path model (PLS-PM) suggested that organic carbon will drive the blackening and odorization process by affecting DO levels and microbial community structure and that the contribution of Desulfobacterota in water to the formation of black and odorous water was higher than that in sediment. Overall, our study provides insights into the characteristics of black and odorous water formation and suggests potential ways to prevent its formation by controlling DOC and inhibiting the growth of Desulfobacterota in water bodies.

Evolution and interaction of microbial communities in mangrove microbial fuel cells and first description of Shewanella fodinae as electroactive bacterium

Understanding exoelectrogenic bacteria mechanisms and their interactions in complex biofilm is critical for the development of microbial fuel cells (MFCs). In this article, assumptions concerning the benefits of the complex sediment microbial community for electricity production were explored with both the complex microbial community and isolates identified as Shewanella. Analysis of the microbial community revealed a strong influence of the sediment community on anodes and electrolytes compared to that of only water. Moreover, while Pelobacteraceae-related genera were dominant in our MFCs instead of Desulfuromonas and Geobacter as usually reported, the electroactive Shewanella algae and Shewanella fodinae were isolated and cultivated from the anodic biofilm. S. fodinae, described for the first time as an electroactive bacterium to the best of our knowledge, led to a maximal current density of 3.6 A/m2 set as 0.3 V/SCE in a three-electrode set-up fed with lactate. S. algae, in a complex medium containing several available substrates, showed several preferential oxidative behaviors including a diauxic behavior. In pure culture and under our conditions, S. fodinae and S. algae were not able to use acetate as a sole electron donor. However, their presence in our acetate-fed MFCs and the adaptive behavior of S. algae hint a syntrophic interaction between the bacteria to optimize the use of the substrate in a complex environment.

Spatio-temporal variation of the microbial community of the coast of Lebanon in response to petroleum hydrocarbon pollution

In this study, the coast of Lebanon was analyzed for the dynamic changes in sediment microbial communities in response to a major petroleum oil spill and tar contamination that occurred in the summer of 2021. Spatio-temporal variations in the microbial structure along the shores of Lebanon were assessed in comparison to baseline microbial structure determined in 2017. Microbial community structure and diversity were determined using Illumina MiSeq technology and DADA2 pipeline. The results show a significant diversity of microbial populations along the Lebanese shore, and a significant change in the sediment microbial structure within four years. Namely, Woeseia, Blastopirellula, and Muriicola were identified in sediment samples collected in year 2017, while a higher microbial diversity was observed in 2021 with Woeseia, Halogranum, Bacillus, and Vibrio prevailing in beach sediments. In addition, the results demonstrate a significant correlation between certain hydrocarbon degraders, such as Marinobacter and Vibrio, and measured hydrocarbon concentrations.

Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution.

Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats

BackgroundArtificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.ResultsThe results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.ConclusionsThis study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

Shifts in sediment bacterial communities reflect changes in depositional environments in a fluviatile context

Sediments are complex heterogeneous matrices allowing to some extent the recording of past environmental conditions by integrating sediment characteristics, contamination and the microbial community assembly. In aquatic environments, abiotic environmental filtering is considered the primary deterministic mechanism shaping microbial communities in sediments. However, the number and relative contributions of geochemical and physical factors associated with biotic parameters (reservoir of microorganisms) complicate our understanding of community assembly dynamics. In this study, the sampling of a sedimentary archive in a site alternately subjected to contrasting inputs from the Eure and the Seine Rivers allowed us to study the response of microbial communities to changes in depositional environment over time. The coupling of the quantification and sequencing of the gene encoding the 16S rRNA with analyses of grain size, organic matter and major and trace metal contents demonstrated that microbial communities reflected contrasting sedimentary inputs over time. Total organic carbon (TOC) was the main factor influencing microbial biomass, while the quantity and quality of organic matter (R400, RC/TOC), major elements (i.e. Al, Fe, Ti) and trace metals (i.e. Zn, Pb, Cu, Cr, Ni, As, Co, Ag, Sb) shaped the structure of the microbial community. Besides the effect of geochemical factors, a specific microbial signature was associated with the contrasting sedimentary sources, highlighting the importance of the microbial reservoir in the assembly of microbial communities. Indeed, the main genera identified in the facies influenced by the Eure River were affiliated with the phyla Desulfobacterota (Syntrophus, Syntrophorhabdus, Smithella, Desulfatiglans), Firmicutes (Clostridium_sensu_stricto_1), Proteobacteria (Crenothrix), Verrucomicrobiota (Luteolibacter), while the contributions of the Seine River were characterised by some halophilic genera Salirhabdus (Firmicutes), Haliangium (Myxococcota) and SCGC-AB-539-J10 (Chloroflexi). This study sheds light on the overall processes determining the assembly of microbial communities in sediments and the importance of associating geochemical factors with reservoirs of microorganisms inherited from sediment sources.

Tropical lacustrine sediment microbial community response to an extreme El Niño event

Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015–2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.

Structure of the river sediment microbiomes impacted by anthropogenic land uses, environmental and spatial variations

River sediments are impacted by anthropogenic land uses since they are the major sinks of pollutants. Sediment microbial communities play vital roles in the degradation of toxic compounds and the recycling of nutrients, sustaining healthy aquatic ecosystems. However, sediment microbiomes impacted by both anthropogenic and natural disturbances are not well documented. This study investigated the dynamics of sediment microbiomes in response to major anthropogenic land uses, environmental, and spatial factors across 25 locations along the Ganh Hao river in Vietnam, using high-throughput sequencing targeting the V3–V4 regions of the 16S rRNA gene. The sediment microbiomes were exclusively dominated by Proteobacteria (59–79%). Microbial taxa associated with shrimp farms, a major land use, were koll13, GCA004, Piscirickettsiaceae, Marinicellaceae, and Desulfobulbaceae. The resulting variation partitioning, based on CCA, indicated that spatial factors highly influenced the microbial profile and explained 41.8% of the microbial variation. However, the variation in sediment microbiomes was largely impacted by a combination of environmental factors (i.e., As, Pb and Cu concentrations, pH and EC) and the presence of shrimp farms which, together with spatial variation, explained 77.4% of the microbial variation. Overall, this study provides insights into the spatial structure of river sediment microbiomes and provides the biological signature of sediment microbiome in response to the major anthropogenic land use and seawater intrusion.

Parabens Increase Sulfamethoxazole-, Tetracycline- and Paraben-Resistant Bacteria and Reshape the Nitrogen/Sulfur Cycle-Associated Microbial Communities in Freshwater River Sediments.

Backgrounds Parabens are pollutants of emerging concern in aquatic environments. Extensive studies regarding the occurrences, fates and behavior of parabens in aquatic environments have been reported. However, little is known about the effects of parabens on microbial communities in freshwater river sediments. This study reveals the effects of methylparaben (MP), ethylparaben (EP), propylparaben (PP) and butylparaben (BP) on antimicrobial-resistant microbiomes, nitrogen/sulfur cycle-associated microbial communities and xenobiotic degrading microbial communities in freshwater river sediments. Methods The river water and sediments collected from the Wai-shuangh-si Stream in Taipei City, Taiwan were used to construct a model system in fish tanks to test the effects of parabens in laboratory. Results Tetracycline-, sulfamethoxazole- and paraben-resistant bacteria increased in all paraben treated river sediments. The order of the overall ability to produce an increment in sulfamethoxazole-, tetracycline- and paraben-resistant bacteria was MP > EP > PP > BP. The proportions of microbial communities associated with xenobiotic degradation also increased in all paraben-treated sediments. In contrast, penicillin-resistant bacteria in both the aerobic and anaerobic culture of paraben-treated sediments decreased drastically at the early stage of the experiments. The proportions of four microbial communities associated with the nitrogen cycle (anammox, nitrogen fixation, denitrification and dissimilatory nitrate reduction) and sulfur cycle (thiosulfate oxidation) largely increased after the 11th week in all paraben-treated sediments. Moreover, methanogens and methanotrophic bacteria increased in all paraben-treated sediments. In contrast, the nitrification, assimilatory sulfate reduction and sulfate-sulfur assimilation associated to microbial communities in the sediments were decreased by the parabens. The results of this study uncover the potential effects and consequences of parabens on microbial communities in a freshwater river environment.