Sediment Bacterial Communities Research Articles

Vertical exchange versus horizontal dispersal in structuring local planktonic and sedimentary bacterial communities in polluted lotic ecosystems

Elucidating the mechanisms underlying community assembly remains a central question in community ecology, especially in aquatic ecosystems disrupted by human activities. Understanding the causes and consequences of community responses to changing environmental conditions is essential for revealing the ecological effects of anthropogenic disturbances and proposing practical strategies for ecological restoration. While stochastic dispersal and species sorting are known to influence local biological communities, most studies have focused on horizontal dispersal, often neglecting the vertical exchange of organisms between planktonic and sedimentary communities when studying stochastic dispersal. We used a highly disturbed urban river in Beijing as a model system to investigate the relative roles of stochastic dispersal versus species sorting driven by local pollution, as well as two components of stochastic dispersal, vertical exchange and horizontal dispersal, in structuring local bacterial communities. Our integrated analyses of planktonic and sedimentary bacterial communities revealed that, despite different spatial patterns along the river, both types of bacterial communities were primarily shaped by stochastic dispersal processes rather than species sorting influenced by the environmental gradient. Notably, in addition to the effect of horizontal dispersal along the river, the vertical exchange between planktonic and sedimentary bacterial communities significantly contributed to the formation of local communities. These findings suggest that both vertical exchange and horizontal dispersal should be considered when assessing the role of stochastic dispersal in shaping local community structure in microbial communities.

Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments

Background: the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks. Objectives: this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023. Methods: the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system. Results: the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water. Conclusions: these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.

Impact of Triclosan on Bacterial Biodiversity and Sediment Enzymes - A Microcosm Study.

Triclosan (TCS), a widely used antimicrobial biocide, has raised serious concern among the scientific community in recent years owing to its ubiquitous presence around the globe and toxicity to aquatic organisms. The current study investigated the alterations in bacterial diversity, nutrients, and sediment enzyme activity in TCS-exposed sediment. TCS concentrations of 3mg/L (T1) and 6mg/L (T2) were applied in a microcosm setup for 28 days to sediment collected from Versova Creek, Mumbai. Among sediment enzymes, dehydrogenase activity exhibited the greatest degree of variability in 3mg/L exposed sediment. Nitrite, total nitrogen and urease exhibited higher concentrations in 6mg/L TCS exposed sediment. The concentration of ammonia was observed to be decreasing in treatments exposed to 6mg/L TCS. Total heterotrophic bacteria exhibited an increase in count in T1 and a decrease in T2. Metagenomics data showed a higher relative abundance of bacteria in T1 compared to T2 on the 28th day of sampling. Proteobacteria was found to be the most abundant phylum in all samples, and their relative abundance was reduced by 0.14% in T1 and 5.48% in T2. The results confirm the alterations in the composition of sediment bacterial communities and their enzymatic activities due to TCS exposure.

Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.

A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.

Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment

Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.

Deciphering the effects of Paracoccus denitrificans on florfenicol degradation and microbial community in sediments

The environmental impacts of antibiotics in sediments, which are a key problem restricting the sustainable development of aquaculture, have been reported extensively. Biological denitrification is a low-cost means to remediate environment. To clarify the the remediation behavior of Paracoccus denitrificans in sewage environment, we studied the changes of bacterial community in sediments polluted by florfenicol after inoculation with P. denitrificans through amplicon technology. Our results showed that P. denitrificans continuously enriched some antibiotic-responsive small RNAs (sRNAs) in promotion of florfenicol degradation, making the abundance of denitrifying functional genes tend to be normalized. Florfenicol and NH4+-N are the main factors affecting bacterial communities regarding the results of redundancy analysis (RDA) and pearson's correlation analysis. In the denitrification-related functional categories, the function of nitrate reduction in the community was obviously enhanced. Furthermore, the risk of pathogen infection induced by florfenicol was reduced. In conclusion, our study exhibited the ability of strain P. denitrificans to degrade florfenicol and bioremediate, which provided a theoretical basis for the application of P. denitrificans in aquaculture industry.

Bacterial Diversity in Sediments from Lianhuan Lake, Northeast China.

Lake microbiota play a crucial role in geochemical cycles, influencing both energy flow and material production. However, the distribution patterns of bacterial communities in lake sediments remain largely unclear. In this study, we used 16S rRNA high-throughput sequencing technology to investigate the bacterial structure and diversity in sediments across different locations (six independent lakes) within Lianhuan Lake and analyzed their relationship with environmental factors. Our findings revealed that both the alpha and beta diversity of sediment bacterial communities varied significantly among the six independent lakes. Furthermore, changes between lakes had a significant impact on the relative abundance of bacterial phyla, such as Pseudomonadota and Chloroflexota. The relative abundance of Pseudomonadota was highest in Habuta Lake and lowest in Xihulu Lake, while Chloroflexota abundance was lowest in Habuta Lake and highest in Tiehala Lake. At the genus level, the relative abundance of Luteitalea was highest in Xihulu Lake compared to the other five lakes, whereas the relative abundances of Clostridium, Thiobacillus, and Ilumatobacter were highest in Habuta Lake. Mantel tests and heatmaps revealed that the relative abundance of Pseudomonadota was significantly negatively correlated with pH, while the abundance of Chloroflexota was significantly positively correlated with total phosphorus and total nitrogen in water, and negatively correlated with electrical conductivity. In conclusion, this study significantly enhances our understanding of bacterial communities in the different lakes within the Lianhuan Lake watershed.

The diversity and biogeography of bacterial communities in lake sediments across different climate zones

Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R2 = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured_f_Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria.

Evaluation of a novel attapulgite loaded sulfidized nanoscale zero-valent iron for immobilization of Pb in sediment: Performance, microenvironmental response, and mechanisms

In recent years, industrial activities involving electroplating and mining have caused Pb to enter rivers and become over-enriched in sediments, posing a potential risk to aquatic organisms. Given this, in this study, attapulgite loaded sulfidized nZVI (S-nZVI@ATP) was prepared by sulfidized modification and ATP loading and applied for the first time to the remediation of Pb contaminated sediments. The immobilization effect and mechanism of S-nZVI@ATP on Pb contaminated sediments were comprehensively investigated, as well as the changes in the microenvironment during the remediation process were assessed. Characterization analysis revealed that S-nZVI was uniformly loaded on the surface of ATP, and the characteristic functional groups of ATP, such as Al/Mg-OH and Si-O, were successfully loaded. Incubation experiments demonstrated that S-nZVI@ATP significantly reduced the availability and leaching toxicity of sediment Pb with immobilization efficiencies as high as 94.08% and 73.15%, respectively (P < 0.05), meanwhile, it facilitated the conversion of acid soluble Pb to the residue state. This phenomenon suggested that S-nZVI@ATP displayed excellent performance in immobilizing Pb. The increase of sediment pH and the decrease of Eh were beneficial to the immobilization of Pb. The addition of S-nZVI@ATP changed the structure and composition of the sediment bacterial community, with Proteobacteria, Firmicutes, and Bacteroidota being the dominant phyla. Except for sucrase, urease and catalase activities were increased by 1.23 and 2.48 times, respectively. Correlation analysis highlighted the importance of pH, Eh, Proteobacteria phylum, and Firmicutes phylum in sediment Pb immobilization. Post-reaction material characterization indicated that the main mechanisms of S-nZVI@ATP for sediment Pb immobilization were adsorption, complexation, ion exchange, electrostatic attraction, reduction and precipitation.

Analysis of bacterial community structure, functional variation, and assembly mechanisms in multi-media habitats of lakes during the frozen period

Ice, water, and sediment represent three interconnected habitats in lake ecosystems, and bacteria are crucial for maintaining ecosystem equilibrium and elemental cycling across these habitats. However, the differential characteristics and driving mechanisms of bacterial community structures in the ice, water, and sediments of seasonally frozen lakes remain unclear. In this study, high-throughput sequencing technology was used to analyze and compare the structure, function, network characteristics, and assembly mechanisms of bacterial communities in the ice, water, and sediment of Wuliangsuhai, a typical cold region in Inner Mongolia. The results showed that the bacterial communities in the ice and water phases had similar diversity and composition, with Proteobacteria, Bacteroidota, Actinobacteria, Campilobacterota, and Cyanobacteria as dominant phyla. The bacterial communities in sediments displayed significant differences from ice and water, with Chloroflexi, Proteobacteria, Firmicutes, Desulfobacterota, and Acidobacteriota being the dominant phyla. Notably, the bacterial communities in water exhibited higher spatial variability in their distribution than those in ice and sediment. This study also revealed that during the frozen period, the bacterial community species in the ice, water, and sediment media were dominated by cooperative relationships. Community assembly was primarily influenced by stochastic processes, with dispersal limitation and drift identified as the two most significant factors within this process. However, heterogeneous selection also played a significant role in the community composition. Furthermore, functions related to nitrogen, phosphorus, sulfur, carbon, and hydrogen cycling vary among bacterial communities in ice, water, and sediment. These findings elucidate the intrinsic mechanisms driving variability in bacterial community structure and changes in water quality across different media phases (ice, water, and sediment) in cold-zone lakes during the freezing period, offering new insights for water environmental protection and ecological restoration efforts in such environments.

Bacterial Communities across Multiple Ecological Niches (Water, Sediment, Plastic, and Snail Gut) in Mangrove Habitats.

Microbial composition across substrates in mangroves, particularly in the Middle East, remains unclear. This study characterized bacterial communities in sediment, water, Terebralia palustris snail guts, and plastic associated with Avicennia marina mangrove forests in two coastal lagoons in the Sea of Oman using 16S rDNA gene MiSeq sequencing. The genus Vibrio dominated all substrates except water. In the gut of snails, Vibrio is composed of 80-99% of all bacterial genera. The water samples showed a different pattern, with the genus Sunxiuqinia being dominant in both Sawadi (50.80%) and Qurum (49.29%) lagoons. There were significant differences in bacterial communities on different substrata, in particular plastic. Snail guts harbored the highest number of unique Operational Taxonomic Units (OTUs) in both lagoons, accounting for 30.97% OTUs in Sawadi and 28.91% OTUs in Qurum, compared to other substrates. Plastic in the polluted Sawadi lagoon with low salinity harbored distinct genera such as Vibrio, Aestuariibacter, Zunongwangia, and Jeotgalibacillus, which were absent in the Qurum lagoon with higher salinity and lower pollution. Sawadi lagoon exhibited higher species diversity in sediment and plastic substrates, while Qurum lagoon demonstrated lower species diversity. The principal component analysis (PCA) indicates that environmental factors such as salinity, pH, and nutrient levels significantly influence bacterial community composition across substrates. Variations in organic matter and potential anthropogenic influences, particularly from plastics, further shape bacterial communities. This study highlights the complex microbial communities in mangrove ecosystems, emphasizing the importance of considering multiple substrates in mangrove microbial ecology studies. The understanding of microbial dynamics and anthropogenic impacts is crucial for shaping effective conservation and management strategies in mangrove ecosystems, particularly in the face of environmental changes.

Plastic debris mediates bacterial community coalescence by breaking dispersal limitation in the sediments of a large river

Plastic debris has recently been proposed as a novel habitat for bacterial colonization, which can raise perturbations in bacterial ecology after burial in riverine sediments. However, community coalescence, as a prevalent process involving the interrelationships of multiple communities and their surrounding environments, has been rarely discussed to reveal the impact of the plastisphere on sedimentary bacterial community. This study analyzed the bacterial community in plastic debris and sediment along the Nujiang River, elucidating the role of the plastisphere in mediating community coalescence in sediments. Our results demonstrated that the plastisphere and sedimentary bacterial communities exhibited distinct biogeography along the river (r = 0.694, p < 0.01). Based on overlapped taxa and SourceTracker, the extent of coalescence between adjacent communities was in following orders: plastic-plastic (0.589) > plastic-sediment (0.561) > sediment-sediment (0.496), indicating the plastisphere promoted bacterial community coalescence along the river. Flow velocity and geographic distance were the major factors driving the plastisphere changes, suggesting that the plastisphere were vulnerable to dispersal. The null model and the neutral model provided additional support for the higher immigration ability of the plastisphere to overcome dispersal limitation, highlighting the potential importance of the plastisphere in community coalescence. Network analysis indicated the critical role of keystone species (Proteobacteria, Bacteroidetes, and Gemmatimonadetes) in mediating the coalescence between sedimentary bacterial community and the plastisphere. In summary, the plastisphere could mediate the coalescence of bacterial communities by overcoming dispersal limitation, which provides new perspectives on the plastisphere altering bacterial ecology in riverine sediments.

Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China.

Volcanic lakes originate from a volcanic crater or caldera, and were a crucial component of aquatic ecosystems. Sediment bacteria play an important role in the nutrient cycling of aquatic ecosystems; however, their patterns distribution in volcanic lakes and the surrounding river habitats are unknown. In this study, we compare the sediment bacterial communities and their co-occurrence networks between these two habitats in the Inner Mongolia Autonomous Region, Northeastern China (the Arxan UNESCO Global Geopark), using 16S rRNA gene amplicon sequencing. The results revealed that there were significant variations in the physicochemical parameters of the sediment between these two habitats. The bacterial α-diversity, β-diversity, and community composition of the sediment also significantly differed between these two habitats. Network analysis showed that the co-occurrence patterns and keystone taxa in the sediment differed between these two habitats. The sediment bacterial communities in the river habitats were more stable than those in the lake habitats in the face of environmental change. Canonical correspondence analysis demonstrated that both physical (pH and MC) and nutrition-related factors (TN, TP, LOI, and TOC) were the most important environmental factors shaping the variations of bacterial community composition (BCC) in the sediment between these two habitats. This work could greatly improve our understanding of the sediment BCC of the sediment from aquatic ecosystems in the UNESCO Global Geopark.

Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China

The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.

Anthropogenic activity shapes the assemble and co-occurrence pattern of microbial communities in fishing harbors around the Bohai economic circle

This study aimed to elucidate the effects of coastal environmental stress on the composition of sediment bacterial communities and their cooccurrence patterns in fishing harbors around the Bohai Economic Circle, China. Compared with the natural sea area, fishing harbors contained higher levels of organic pollution (organic pollution index = 0.12 ± 0.026) and considerably reduced bacterial richness and evenness. The distributions of sediment microbial communities clustered along the pollutant concentration gradients across fishing harbors. Betaproteobacteria dominated (76%) organically polluted fishing harbors, which were mostly disturbed by anthropogenic activities. However, the harbors also revealed the absence of numerous pathogenic (Coxiella and Legionella) and photosynthetic (Synechococcus and Leptolyngbya) bacteria. Abundant genera, including Thiobacillus and Arenimonas, exhibited a positive correlation with total phosphorus and a negative correlation with total nitrogen in sediments. Meanwhile, Sulfurovum, Psychrobacter, and Woeseia showed the opposite trend. Pollutant accumulation and anthropogenic activities caused the decrease in the sediment microbial diversity and dispersal ability and promoted convergent evolution. Severely polluted harbors with simplified cooccurrence networks revealed the presence of destabilized microbial communities. In addition, the modularity of bacterial networks decreased with organic pollution. Our results provide important insights into the adjustment mechanism of microbial communities to community organization and functions under environmental pollution stress. Overall, this study enhanced our understanding of how microbial communities in coastal sediments adapted and survived amidst anthropogenic activities like oily effluent discharges from large ships, wash water, domestic sewage, garbage, and fisheries wastes. It also examined their resilience to future contamination.

Immobilization of phosphorus in sediment-water system by hydrous iron oxide and hydrous iron oxide/calcite mixture under feed input condition

The efficiency and mechanism of hydrous iron oxide (HFO) and HFO/calcite mixture to inactivate the phosphorus in the overlying water (OW)/sediment system under the feed adding condition were explored, and the effect of HFO and HFO/calcite mixture addition on the diversity, composition and function of bacterial communities in the sediment was examined. HFO and HFO/calcite mixture direct addition can effectively lower the concentration of soluble reactive phosphorus (RSP) and diffusion gradient in thin film-unstable phosphorus (PDGT) in OW and inactivate the PDGT in the upper sediment. The elimination efficiencies of RSP by the direct HFO and HFO/calcite mixture addition were 48.9–97.0 % and 42.4–95.4 %, respectively. The alteration in the addition mode from the one-time to multiple direct addition was beneficial to the immobilization of RSP and PDGT in OW and PDGT in the upper sediment by HFO and HFO/calcite mixture under the feed input condition in the long run. Permeable fabric wrapping reduced the inactivation efficiency of RSP in OW by HFO and HFO/calcite mixture, but it made the recycling of these materials possible. Most of P immobilized by HFO and HFO/calcite mixture was relatively or very stable. After the HFO and HFO/calcite mixture addition, the composition of bacterial communities in the surface sediment changed. However, the bacterial communities in the amended sediments still can perform good ecological function. Our findings suggest that HFO and HFO/calcite mixture are promising phosphorus-immobilization materials for the inactivation of RSP and PDGT in OW and PDGT in the upper sediment under the feed inputting condition.

Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water.

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

Effects of polypropylene films and leached dissolved organic matters on bacterial community structure in mangrove sediments

Over the past decades, the accumulation of plastics in mangrove ecosystems has emerged as a significant environmental concern, primarily due to anthropogenic activities. Polypropylene (PP) films, one of the plastic types with the highest detection rate, tend to undergo intricate aging processes in mangrove ecosystems, leading to the release of dissolved organic matter (DOM) that may further influence the local bacterial communities. Yet, the specific effects of new and weathered (aged) plastic films and the associated leached DOM on bacterial consortia in mangrove sediments remain poorly understood. In this study, an incubation experiment was conducted to elucidate the immediate effects and mechanisms of the new and relatively short-term (45 or 90 days) aged PP films, as well as their leached DOM (PDOM), on characteristics of DOM and the bacterial community structure in mangrove sediments under different tidal conditions. Surface morphology and functional group analyses showed that both new and aged PP films exhibited comparable degradation profiles under different tidal conditions over the incubation period. As compared to the new PP film treatments, the introduction of the short-term aged PP films significantly affected the content of humic-like compounds in sediments, and such effects were partially ascribed to the release of PDOM during the incubation. Although the addition of PP films and PDOM showed minor effects on the overall diversity and composition of bacterial communities in the sediments, the abundance of some dominant phyla exhibited a growth or reduction tendency, possibly changing their ecological functions. This study was an effective attempt to investigate the relationship among plastic surface characteristics, sedimentary physicochemical properties, and bacterial communities in mangrove sediments. It revealed the ecological ramifications of new and short-term plastic pollution and its leachates in mangrove seedtimes, enhancing our understating of their potential impacts on the health of mangrove ecosystems.

Profiling sediment bacterial communities and the response to pattern-driven variations of total nitrogen and phosphorus in long-term polyculture ponds

Sediment bacterial communities are decisive drivers of nutrient cycling processes in aquaculture ecosystems and are readily affected by surrounding environmental factors. However, the knowledge of sediment nutrient accumulations and bacterial community structure is limited in the emerging polyculture systems. Herein, we investigated the profiles of sediment properties and bacterial communities in six typical polyculture ponds and primarily explored the influence of total nitrogen and phosphorus on the bacterial species and diversity. In almost all sediment samples, Proteobacteria, Chloroflexi, and Bacteroides were the dominant species at the phylum level, and the five most abundant bacterial genera were Sulfurovum, Woeseia, Ilumatobacter, Robiginitalea, and Cyanobium_PCC-6307. A clear different bacterial community was observed with the most dominant bacterial phylum Firmicutes and the lowest bacterial diversity in TZ1 pond sediment; meanwhile, the TZ1 pond also showed the highest TN and TP concentrations. Notably, sediments from WZ1 and WZ2 ponds in low-latitude regions exhibited higher bacterial richness and diversity. Based on Pearson’s correlation analysis, bacterial α-diversity indices showed significant negative correlation with sediment TP content, and TN content contributed the most to the abundance of sediment dominant bacterial genus, indicating that the bacterial community is highly associated with sediment nutrient concentrations. Moreover, co-occurrence network analysis further revealed some keystone taxa that exhibited high correlations with other bacterial species, especially the high-abundance genus Robiginitalea bridging a large number of connections. Compared to traditional mono-mariculture pattern, our study provided direct evidence of lower nutrient loadings and different bacterial communities in the polyculture ponds. This could assist polyculture practitioners in developing effective strategies for detailed nutritional management.

Diversity of Bacterial Communities in Sediment in Inland Water Bodies in Relation to Environmental Factors and Human Impacts: A Case Study on Typical Regions in Vietnam

Environmental changes and human impact can alter biodiversity in negative manners that affect mankind’s sustainable development. Particularly, such effects on inland waters are even more concerning, as those ecosystems play essential roles in sustaining human life as well as relevant wildlife. Thus, in this study, we investigated such effects on microbial diversity in inland waters in Vietnam using bacterial communities in sediment as indicators. To do this, we collected sediment samples from various locations in three respective regions (Red river in the north, Ba river in the central area, and Mekong delta flood zone in the south) using standard methods, extracted their total DNA, sequenced their V3-V4 16S rRNA gene fragments using an Illumina Miseq platform and analyzed the sequences to infer the diversity of the bacterial communities in the samples. These communities were compared in terms of richness (alpha diversity) and composition (beta diversity), and the correlations between their diversity levels and environmental factors, as well as human activities, were analyzed by using standard statistical tools. Our results showed that the communities were different from each other solely by region, in richness and critically in composition, although there were some communities distinctively different from all the others. Among environmental factors, only water salinity (and conductivity) had negative correlations with alpha-diversity indices of the bacterial communities, and phosphate concentration and turbidity had positive correlations, while the other factors had almost no correlations, which partially explains the region-specific diversity. These results also suggest that climate change incidences, especially sea intrusion, can have significant effects on microbial diversity in inland waters. The impact of human activities did not appear severe, solely affecting bacterial community richness, but not significantly affecting bacterial community composition. However, apparently reduced bacterial diversity in several sites with intense human impacts and distinct environmental conditions should be noted and deserve further investigation.