Biogeography and Diversity of Freshwater Bacteria on a River Catchment Scale

A mica filter enables bacterial enrichment from large volumes of natural water for sensitive monitoring of pathogens by nanopore sequencing

Nanopore sequencing is extremely promising for the high-throughput detection of pathogenic bacteria in natural water; these bacteria may be transmitted to humans and cause waterborne infectious diseases. However, the concentration of pathogenic bacteria in natural water is too low to be detected directly by nanopore sequencing. Herein, we developed a mica filter to enrich over 85% of bacteria from > 10 L of natural water in 100 min, which led to a 102-fold improvement in the assay limits of the MinION sequencer for assessing pathogenic bacteria. Correspondingly, the sequencing time of S. Typhi detection at a concentration as low as 105 CFU/L was reduced from traditional 48 h to 3 h. The bacterial adsorption followed pseudo-first-order kinetics and the successful adsorption of bacteria to the mica filter was confirmed by scanning electron microscopy and Fourier infrared spectroscopy et al. The mica filter remained applicable to a range of water samples whose quality parameters were within the EPA standard limits for freshwater water. The mica filter is thus an effective tool for the sensitive and rapid monitoring of pathogenic bacteria by nanopore sequencing, which can provide timely alerts for waterborne transmission events.

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria

The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the 'Alpavirinae', 'Amoyvirinae', and Gokushovirinae. We have isolated 'Ascunsovirus oldenburgi' ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named 'Tainavirinae' and 'Occultatumvirinae'. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.

The Geochemical Drivers of Bacterial Community Diversity in the Watershed Sediments of the Heihe River (Northern China)

The city of Zhangye (Gansu Region, China) has been subjected to several changes related to the development of new profitable human activities. Unfortunately, this growth has led to a general decrease in water quality due to the release of several toxic wastes and pollutants (e.g., heavy metals) into the Heihe River. In order to assess the environmental exposure and the potential threat to human health, microbiological diversity for the monitoring of water pollution by biotic and abiotic impact factors was investigated. In particular, we analysed samples collected on different sites using 454 pyrotag sequencing of the 16S ribosomal genes. Then, we focused on alpha-diversity indices to test the hypothesis that communities featuring lower diversity show higher resistance to the disturbance events. The findings report that a wide range of environmental factors such as pH, nutrients and chemicals (heavy metals (HMs)), affected microbial diversity by stimulating mutualistic relationships among bacteria. Furthermore, a selection in bacterial taxa related to the different concentrations of polluting compounds was highlighted. Supporting the hypothesis, our investigation highlights the importance of microbial communities as sentinels for ecological status diagnosis.

Compositional Changes and Co-Occurrence Patterns of Planktonic Bacteria and Microeukaryotes in a Subtropical Estuarine Ecosystem, the Pearl River Delta

Planktonic microorganisms in aquatic ecosystems form complex assemblages of highly interactive taxa and play key roles in biogeochemical cycles. However, the microbial interactions within bacterial and microeukaryotic communities, and the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances in the river estuary remain unknown. Here, 16S and 18S rRNA gene sequencing were used to investigate the compositional changes and the co-occurrence patterns of bacterial and microeukaryotic communities. The results showed that the rare taxa in the bacterial communities were more prevalent than those in the microeukaryotic communities and may influence the resilience and resistance of microorganisms to environmental variations in estuarine ecosystems. The environmental variations had strong effects on the microeukaryotic communities and their assembly mechanisms but not on the bacterial communities in our studied area. However, based on co-occurrence network analyses, the bacterial communities had stronger links and more complex interactions than microeukaryotic communities, suggesting that bacterial networks may help improve the buffering capacities of the estuarine ecosystem against environmental change. The keystone taxa of bacteria mainly belonged to rare subcommunities, which further illustrates that rare taxa may play fundamental roles in network persistence. Overall, these results provide insights into the microbial responses of aquatic ecosystems to environmental heterogeneity.

When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment

In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.

Patterns of Structural and Functional Bacterioplankton Metacommunity along a River under Anthropogenic Pressure

Bacteria, an integral part of aquatic ecosystems, are responsible for the circulation of matter and flow of energy. Since bacterioplankton rapidly responds to any natural and human-induced disturbances in the environment, it can serve as a bioindicator of these changes. Knowing factors that shape the microbial community structure may help the sustainable management of the water environment. However, the identification of environmental signals affecting the structure and function of bacterioplankton is still a challenge. The study analyses the impact of environmental variables on basic microbial parameters, which determines the effectiveness of ecological processes in rivers. Measurements of bacterioplankton abundance (BA) and extracellular enzyme activity (EEA) were based on fluorescent markers. The bacterial community structure was determined by 16S rRNA gene amplicon sequencing (Illumina). The results indicate spatial variation in bacterioplankton abundance. Temporal variation was not significant. Lipase and aminopeptidase had the highest level of activity. EEA was not correlated with bacterial abundance but was significantly correlated with temperature. Moreover, differences in lipase, α-glucosidase and β-glucosidase activity levels between spring and summer were noted. At the same time, the location of sampling site had a significant influence on aminopeptidase activity. The taxonomic analysis of bacterioplankton communities in the Brda River indicated that, although different numbers of OTUs were recorded in the studied river sections, bacterioplankton biodiversity did not change significantly along the river with distance downstream. Anthropogenically modified river sections were characterized by the dominance of Flavobacterium (Bacterioidetes) and hgcl clade (Actinobacteria) taxa, known for their ability to produce extracellular enzymes. PCoA analysis revealed that the sites located in the lower river course (urban area) had the most similar bacterial community structure (β-diversity). The study provides new insight into the changes in microbial communities along the river and emphasizes the potential impact of anthropogenization on these processes.

Effect of Maize Straw Biochar on Bacterial Communities in Agricultural Soil

Biochar has become a popular soil amendment. However, its effect on soil microbial community is still unclear. In the present study, maize straw biochar was pyrolysed at 300°C, 450°C and 600°C, respectively, and then was added to agricultural soil at the ratio of 0.5%, 1% and 2%. Bacterial dynamics was analyzed in the pot experiments using denaturing gradient gel electrophoresis. The results indicated that the pyrolysis temperature has great impact on the elemental composition, pH and porous structures of biochar. Moreover, pyrolysis temperature was primary factor to drive the variation of bacterial community structure in biochar amended soil. In addition, the results suggested that biochar amendments on agricultural soil would decrease the bacterial diversity, and selectively promote growth of functional bacteria to become the dominant community, which could increase the bacterial community organization and improve the stability of bacteria to counteract effects of perturbation.