Aquatic Microbial Communities Research Articles

Seasonal shifts in microbial diversity in the lakes of Fildes Peninsula, King George Island, Maritime Antarctica

AbstractFildes Peninsula, on King George Island, has been greatly influenced by recent rapid climate warming. Lakes are pervasive features of Fildes Peninsula landscapes, some of which are used as water sources for Antarctic stations. We studied seven Fildes Peninsula lakes to explore differences among lakes and between seasons in phytoplankton and bacterioplankton communities. We measured environmental variables, analysed pigments using high-performance liquid chromatography and examined bacterial DNA through high-throughput sequencing of the 16S rRNA gene. The main driver structuring microbial communities was the season (i.e. spring vs autumn). Chlorophyceae were the dominant phytoplankton group in all lakes and both seasons. Indicator bacteria for each season were identified, including Flavobacterium, Polaromonas and Oxalobacteraceae as indicators of spring conditions under thick ice, whereas Frankiales and Verrucomicrobia were indicator species of autumn following the ice-free summer. The indicator species for spring are generally observed in oligotrophic conditions, whereas many of the autumn indicators are commonly found in soils. There were lesser between-lake differences in microbial communities in autumn, at the end of the open-water period, than in spring at the end of the ice-covered period. This study will act as the basis for future assessments of changes in aquatic microbial communities.

Compact and automated eDNA sampler for in situ monitoring of marine environments

Using environmental DNA (eDNA) to monitor biodiversity in aquatic environments is becoming an efficient and cost-effective alternative to other methods such as visual and acoustic identification. Until recently, eDNA sampling was accomplished primarily through manual sampling methods; however, with technological advances, automated samplers are being developed to make sampling easier and more accessible. This paper describes a new eDNA sampler capable of self-cleaning and multi-sample capture and preservation, all within a single unit capable of being deployed by a single person. The first in-field test of this sampler took place in the Bedford Basin, Nova Scotia, Canada alongside parallel samples taken using the typical Niskin bottle collection and post-collection filtration method. Both methods were able to capture the same aquatic microbial community and counts of representative DNA sequences were well correlated between methods with R^{2} values ranging from 0.71–0.93. The two collection methods returned the same top 10 families in near identical relative abundance, demonstrating that the sampler was able to capture the same community composition of common microbes as the Niskin. The presented eDNA sampler provides a robust alternative to manual sampling methods, is amenable to autonomous vehicle payload constraints, and will facilitate persistent monitoring of remote and inaccessible sites.

Isolation and characterization of algicidal bacteria from freshwater aquatic environments in China.

Algicidal bacteria can inhibit the growth of algae or lyse algal cells, thus playing roles in shaping aquatic microbial communities and maintaining the functions of aquatic ecosystems. Nevertheless, our understanding of their diversities and distributions remains limited. In this study, we collected water samples from 17 freshwater sites in 14 cities in China and screened a total of 77 algicidal bacterial strains using several prokaryotic cyanobacteria and eukaryotic algae as target strains. According to their target-specificities, these strains were classified into three subgroups, cyanobacterial algicidal bacteria, algal algicidal bacteria, and broad-target algicidal bacteria, each displaying distinctive compositions and geographical distribution patterns. They are assigned to Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes bacterial phyla, of which Pseudomonas and Bacillus are the most abundant gram-negative and gram-positive genus, respectively. A number of bacterial strains, such as Inhella inkyongensis and Massilia eburnean, are suggested as new algicidal bacteria. The diverse taxonomies, algal-inhibiting abilities and distributions of these isolates have suggested that there are rich algicidal bacterial resources in these aquatic environments. Our results provide new microbial resources for algal-bacterial interaction studies, and shed new insights into how algicidal bacteria can be used in the control of harmful algal blooms, as well as in algal biotechnology.

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function

BackgroundThe freshwater microbiome regulates aquatic ecological functionality, nutrient cycling, pathogenicity, and has the capacity to dissipate and regulate pollutants. Agricultural drainage ditches are ubiquitous in regions where field drainage is necessary for crop productivity, and as such, are first-line receptors of agricultural drainage and runoff. How bacterial communities in these systems respond to environmental and anthropogenic stressors are not well understood. In this study, we carried out a three year study in an agriculturally dominated river basin in eastern Ontario, Canada to explore the spatial and temporal dynamics of the core and conditionally rare taxa (CRT) of the instream bacterial communities using a 16S rRNA gene amplicon sequencing approach. Water samples were collected from nine stream and drainage ditch sites that represented the influence of a range of upstream land uses.ResultsThe cross-site core and CRT accounted for 5.6% of the total number of amplicon sequence variants (ASVs), yet represented, on average, over 60% of the heterogeneity of the overall bacterial community; hence, well reflected the spatial and temporal microbial dynamics in the water courses. The contribution of core microbiome to the overall community heterogeneity represented the community stability across all sampling sites. CRT was primarily composed of functional taxa involved in nitrogen (N) cycling and was linked to nutrient loading, water levels, and flow, particularly in the smaller agricultural drainage ditches. Both the core and the CRT were sensitive responders to changes in hydrological conditions.ConclusionsWe demonstrate that core and CRT can be considered as holistic tools to explore the temporal and spatial variations of the aquatic microbial community and can be used as sensitive indicators of the health and function of agriculturally dominated water courses. This approach also reduces computational complexity in relation to analyzing the entire microbial community for such purposes.

Eutrophic water remediation efficiency of algicidal bacteria, Cellvibrio sp. G1 and Chitinimonas sp. G2, and their influence on microbial community structure

Algal blooms that occur periodically in rivers, lakes, and reservoirs are associated with the cumulative effects of excess nutrients from industrial and agricultural development. Algicidal bacteria can be used as environmentally friendly biocontrol agents to manage harmful algal blooms in eutrophic water. However, there is still a dearth of studies on the effects of mixed algicidal agents, the persistence of algae removal efficiency, and the impacts on native aquatic microbial communities. Two strains of algicidal bacteria, Cellvibrio sp. G1 and Chitinimonas sp. G2, were previously isolated and purified from reservoir sediment. Herein, G1 and G2 broth cultures, alone and in combination (1:1, V/V), were added to eutrophic water collected from a park at the volume ratio of 5 %. Eutrophic water remediation efficiency under different treatments was monitored for 30 days, and microbial community dynamics in water were analyzed by full-length sequencing of the 16S rRNA genes. The best algae removal efficiency was observed in the water treated with G1 alone, as indicated by the highest algae removal rate of 41.3 %. The total nitrogen removal rates of G1, G2, and their combination were 33.47 %, 23.65 %, and 28.88 %, respectively; ammonia‑nitrogen removal rates were 24.11 %, 25.02 %, and 19.63 %, respectively; total phosphorus removal rates were 24.11 %, 25.02 %, and 19.63 %, respectively; and orthophosphate removal rates were 46.11 %, 44.37 %, and 27.92 %, respectively. In the water treated with G1 and/or G2, the major genera with algicidal capacity (i.e., Cellvibrio and Chitinimonas) were outcompeted by the well adapted genera (e.g., Pseudomonas). At the late stages of treatment, the algicidal genera decreased in relative abundance, leading to decline in algae removal efficiency and increase in chlorophyll concentration. Based on both eutrophic water remediation efficiency and environmental adaptability, G1 alone was superior to G2 alone or in combination with G1, thus having potential practical implications.

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum.

Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.

Effects of erythromycin and roxithromycin on river periphyton: Structure, functions and metabolic pathways

Macrolides have been frequently detected in the surface waters worldwide, posing a threat to the aquatic microbes. Several studies have evaluated the ecotoxicological effects of macrolides on single algal and bacterial strains. However, without considering the species interaction in the aquatic microbial community, these results cannot be extrapolated to the field. Thus, the present study aimed to evaluate the effects of two macrolides (erythromycin and roxithromycin) on the structure, photosynthetic process, carbon utilization capacity, and the antibiotic metabolic pathways in river periphyton. The colonized periphyton was exposed to the graded concentration (0 μg/L (control), 0.5 μg/L (low), 5 μg/L (medium), 50 μg/L (high)) of ERY and ROX, respectively, for 7 days. Herein, high levels of ERY and ROX altered the community composition by reducing the relative abundance of Chlorophyta in the eukaryotic community. Also, the Shannon and Simpson diversity indexes of prokaryotes were reduced, although similar effects were seldomly detected in the low and medium groups. In contrast to the unchanged carbon utilization capacity, the PSII reaction center involved in the periphytic photosynthesis was significantly inhibited by macrolides at high levels. In addition, both antibiotics had been degraded by periphyton, with the removal rate of 51.63–66.87% and 41.85–48.27% for ERY and ROX, respectively, wherein the side chain and ring cleavage were the main degradation pathways. Overall, this study provides an insight into the structural and functional toxicity and degradation processes of macrolides in river periphyton.–

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis.

Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.

Ecological landscape explains aquifers microbial structure

Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.

Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community

Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.

An Overview of the Impact of Pharmaceuticals on Aquatic Microbial Communities.

Pharmaceuticals are present as pollutants in several ecosystems worldwide. Despite the reduced concentrations at which they are detected, their negative impact on natural biota constitutes a global concern. The consequences of pharmaceuticals' presence in water sources and food have been evaluated with a higher detail for human health. However, although most of the pharmaceuticals detected in the environment had not been designed to act against microorganisms, it is of utmost importance to understand their impact on the environmental native microbiota. Microbial communities can suffer serious consequences from the presence of pharmaceuticals as pollutants in the environment, which may directly impact public health and ecosystem equilibrium. Among this class of pollutants, the ones that have been studied in more detail are antibiotics. This work aims to provide an overview of the impacts of different pharmaceuticals on environmental biofilms, more specifically in biofilms from aquatic ecosystems and engineered water systems. The alterations caused in the biofilm function and characteristics, as well as bacteria antimicrobial tolerance and consequently the associated risks for public health, are also reviewed. Despite the information already available on this topic, the need for additional data urges the assessment of emerging pollutants on microbial communities and the potential public health impacts.

Spatiotemporal heterogeneity of nitrogen transformation potentials in a freshwater estuarine system

Under the influence of water diversion, the microbial community composition of estuarine waters and sediments might have complex spatiotemporal variations. Microbial interactions with N are significant for lake water quality. Therefore, the largest lake receiving seasonal water diversion in the North China Plain was selected as the study area. Based on 16S rRNA high-throughput sequencing and metagenomic sequencing techniques, this study analysed temporal (June–December) and spatial (estuary-pelagic zone) changes in the microbial community and functional gene composition of water and sediment. The results showed that the water microbial community composition had temporality, while sediment microbes had spatiality. The main causes of temporality in the aquatic microbial community were temperature and nitrate-N concentration, while those of sediment were flow velocity and N content. Additionally, there were complex interactions between microbial communities and N. In water, temporal variation in the relative abundance of N-related functional genes might have indirectly contributed to inorganic N composition in June (nitrite-N > ammonia-N > nitrate-N) and August (nitrite-N > nitrate-N > ammonia-N). High nitrate-N concentrations in December influenced the microbial community composition. In sediment, the estuary had higher N functional genes than the pelagic estuary, creating a relatively active N cycle and reducing total N levels in the estuary. This study revealed a potentially overlooked N sink and a flow velocity threshold that has great impacts on microbial community composition. This research contributes to a deeper understanding of the estuarine N cycle under the influence of water diversions, with implications for the calculation of global N balances and the management of lake water environments.

Change of the structure and assembly of bacterial and photosynthetic communities by the ecological engineering practices in Dianchi Lake

Cyanobacterial bloom challenges the aquatic ecosystem and ecological restoration is an effective approach for cyanobacterial bloom control, but the change of aquatic community after ecological restoration is still unclear. Dianchi Lake is an eutrophic lake with frequent cyanobacterial blooms in China, and recent ecological restoration projects in Caohai (north part) have a satisfactory performance. In this study, we collected 249 water samples at 23 sites from Dianchi Lake to explore the relationships between water physicochemical variables and aquatic microbial communities. Water physicochemical variables in Waihai (south part) intensively changed along time, whereas those in Caohai did not. Photoautotrophic communities were significantly divergent between Caohai and Waihai. Waihai had a lower diversity of photoautotrophic community, containing higher abundance of Cyanophyceae (89.9%) than Caohai (42.7%). Nutrient level and Cyanophyceae only exhibited strong correlations in Wahai (p < 0.05). Redundancy analysis and microbial ecological network suggested that microbial communities in Caohai had a higher stability. Deterministic process dominated the microbial assembly (50–80% for bacteria and >90% for photoautotrophs), and particularly in Caohai. Our results unraveled that the structure and assembly of bacterial and photoautotrophic communities significantly changed after ecological restoration, offering valuable suggestions that photosynthetic diversity should be focused for other ecological restoration projects.

Network analysis reveals microbe-mediated impacts of aeration on deep sediment layer microbial communities.

Over-aeration is a common remediation strategy for black and odorous water bodies, in which oxygen is introduced to impact aquatic microbial communities as an electron acceptor of high redox potential. In this study, black-odorous freshwater sediments were cultured for 9 weeks under aeration to investigate microbial covariations at different depths and time points. Based on community 16S rRNA gene sequencing, the microbial covariations were visualized using phylogenetic microbial ecological networks (pMENs). In the spatial scale, we identified smaller and more compact pMENs across all layers compared with the anaerobic control sediments, in terms of network size, average node connectivity, and modularity. The aerated middle layer had the most connectors, the least module hubs, a network hub, shorter average path length, and predominantly positive covariations. In addition, a significant sulfate accumulation in the aerated middle layer indicated the most intense sulfide oxidation, possibly because aeration prompted sediment surface Desulfobulbaceae, known as cable bacteria, to reach the middle layer. In the time scale, similarly, aeration led to smaller pMEN sizes and higher portions of positive covariations. Therefore, we conclude that elevated dissolved oxygen at the water-sediment interface may impact not only the surface sediment but also the subsurface and/or deep sediment microbial communities mediated by microorganisms, particularly by Desulfobulbaceae.

Seasonal changes driving shifts of aquatic rhizosphere microbial community structure and the functional properties

Ecological floating beds could enable roots to become suspended and this allowed submerged roots to harbour various types of microbes. But, there was a lack of systematic research on microbial community structure changes and the influencing mechanisms. In this study, the ecological floating beds were constructed using selected plants [Cyperus involucratus Rottboll (Cyp), Thalia dealbata Fraser (Tha) and Iris tectorum Maxim (Iri)] that was compared with a control group [static water (S)]. The results showed that the highest abundance and diversity of root microbial communities were found in autumn, with the dominant taxa being Proteobacteria, Actinobacteriota, Cyanobacteria, Chloroflexi, Firmicutes, Bacteroidota, and Acidobacteriota. The microbial communities of Tha and Cyp groups greatly overlapped, while the Iri and control groups exhibited distinctly diverse communities. The root microbial populations of the same plant also reflected a large change in different seasons. Conversely, photosynthetic autotrophs and specialized anaerobes were more inclined to thrive at higher temperatures and lower DO concentrations and then they gradually became the dominant species. Microbial co-occurrences of the Tha and control groups were complex and showed both cooperation and competition. In addition, TOC was an important environmental factor that shaped the microbial community structures and DO changed the microbial community by affecting the abundance of aerobic and anaerobic bacteria. Microorganisms showed potential for degradation and metabolism of non-food substances with low/no corresponding metabolic pathways.

Spatiotemporal changes of bacterial communities during a cyanobacterial bloom in a subtropical water source reservoir ecosystem in China

Cyanobacterial blooms, which not only threaten the health and stability of aquatic ecosystems but also influence the microbial community within, emerges as one of the most concerning problems in China. However, how cyanobacterial blooms affect the spatiotemporal variation of aquatic microbial communities remains relatively unclear. In this study, we used high-throughput sequencing to investigate how the cyanobacterial and bacterial community spatiotemporally vary along with main cyanobacterial bloom phases in upstream rivers of a eutrophicated water source reservoir. Both cyanobacterial and bacterial diversities in each river were significantly lower (P < 0.05) during the bloom outbreak phase, showing the apparent influence of cyanobacterial bloom. Dominant cyanobacterial taxa included Cyanobacteriales and Synechococcales, and dominant bacterial taxa comprised Acinetobacter, CL500-29, hgcI clade, Limnohabitans, Flavobacterium, Rhodoluna, Porphyrobacter, Rhodobacter, Pseudomonas, and Rhizobiales, whose changes of relative abundance along with the bloom indicated distinct community composition. Non-metric multidimensional scaling analysis proved that community composition had significant difference amongst bloom phases. Linear discriminant analysis (LDA) with LDA effect size analysis (LEfSe) identified unique dominant cyanobacterial and bacterial OTUs at different phases in each river, indicating spatiotemporal variations of communities. Canonical correlation analysis or redundancy analysis revealed that at different bloom phases communities of each river had distinct correlation patterns with the environmental parameters (temperature, ammonium, nitrate, and total phosphorus etc.), implying the spatial variations of microbial communities. Overall, these results expand current understanding on the spatiotemporal variations of microbial communities due to cyanobacterial blooms. Microbial interactions during the bloom may shed light on controlling cyanobacterial blooms in the similar aquatic ecosystems.

Soil mesofauna alter the balance between stochastic and deterministic processes in the plastisphere during microbial succession

Plastic debris, as a novel substrate, provides an avenue for enriching microbial growth. Although the structure of the aquatic plastisphere microbial community is well-characterised, linkages between microbial community assembly and species co-existence in the soil plastisphere vary and remain poorly understood, particularly when soil fauna is involved. This study investigated the soil plastisphere community, including bacteria, fungi, and protists, focusing on microbial succession and community assembly processes impacted by soil mesofauna. Certain soil plastisphere microbial taxa thrived at particular time points (e.g. Actinobacteria at 60 d), indicating the irreplaceable role of microplastic selection for time-sensitive taxa. Additionally, the biodiversity of keystone ecological clusters in the soil plastisphere was significantly associated with incubation time. Furthermore, the slopes of bacterial and fungal time-decay curves in soil plastisphere were steeper when treated with soil mesofauna than without soil mesofauna, whereas protist time-decay curves (total and abundant taxa) exhibited the opposite trend. Soil mesofauna increased the relative importance of determinacy in the soil plastisphere bacterial assembly process, while enhancing the stochasticity of fungal and protistan community assemblages. The study demonstrates the complex assembly patterns of soil plastisphere microbial communities, emphasising the importance of interactions between the plastisphere and local soil fauna from an ecological perspective.

Next-Generation High-Throughput Sequencing to Evaluate Bacterial Communities in Freshwater Ecosystem in Hydroelectric Reservoirs.

The quality of aquatic ecosystems is a major public health concern. The assessment and management of a freshwater system and the ecological monitoring of microorganisms that are present in it can provide indicators of the environment and water quality to protect human and animal health. with bacteria is. It is a major challenge to monitor the microbiological bacterial contamination status of surface water associated with anthropogenic activities within rivers and freshwater reservoirs. Understanding the composition of aquatic microbial communities can be beneficial for the early detection of pathogens, improving our knowledge of their ecological niches, and characterizing the assemblages of microbiota responsible for the degradation of contaminants and microbial substrates. The present study aimed to characterize the bacterial microbiota of water samples collected alongside the Madeira River and its small tributaries in rural areas near the Santo Antonio Energia hydroelectric power plant (SAE) reservoir in the municipality of Porto Velho, Rondonia state, Western Brazil. An Illumina 16s rRNA metagenomic approach was employed and the physicochemical characteristics of the water sample were assessed. We hypothesized that both water metagenomics and physicochemical parameters would vary across sampling sites. The most abundant genera found in the study were Acinetobacter, Deinococcus, and Pseudomonas. PERMANOVA and ANCOM analysis revealed that collection points sampled at the G4 location presented a significantly different microbiome compared to any other group, with the Chlamidomonadaceae family and Enhydrobacter genus being significantly more abundant. Our findings support the use of metagenomics to assess water quality standards for the protection of human and animal health in this microgeographic region.

Effects of alder- and salmon-derived nutrients on aquatic bacterial community structure and microbial community metabolism in subarctic lakes.

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r2 = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r2 = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity.

Spatial and Seasonal Variations in the Bacterial Community of an Anthropogenic Impacted Urban Stream.

Environmental changes and human activities can alter the structure and diversity of aquatic microbial communities. In this work, we analyzed the bacterial community dynamics of an urban stream to understand how these factors affect the composition of river microbial communities. Samples were taken from a stream situated in Buenos Aires, Argentina, which flows through residential, peri-urban horticultural, and industrial areas. For sampling, two stations were selected: one influenced by a series of industrial waste treatment plants and horticultural farms (PL), and the other influenced by residential areas (R). Microbial communities were analyzed by sequence analysis of 16S rRNA gene amplicons along an annual cycle. PL samples showed high nutrient content compared with R samples. The diversity and richness of the R site were more affected by seasonality than those of the PL site. At the amplicon sequence variants level, beta diversity analysis showed a differentiation between cool-season (fall and winter) and warm-season (spring and summer) samples, as well as between PL and R sites. This demonstrated that there is spatial and temporal heterogeneity in the composition of the bacterial community, which should be considered if a bioremediation strategy is applied. The taxonomic composition analysis also revealed a differential seasonal cycle of phototrophs and chemoheterotrophs between the sampling sites, as well as different taxa associated with each sampling site. This analysis, combined with a comparative analysis of global rivers, allowed us to determine the genera Arcobacter, Simplicispira, Vogesella, and Sphingomonas as potential bioindicators of anthropogenic disturbance.