Biodiversity Of Microbial Communities Research Articles

The Impact of Sewage-Sludge- and Olive-Mill-Waste-Derived Biochar Amendments to Tomato Cultivation

This study elucidated the impact of sewage-sludge (SS) and olive-mill-waste (OMW) biochar amendments to soil using tomatoes as a test crop. Four treatments were evaluated: the “control” with no biochar amendment, two SS biochar treatments with the addition of 10 t/ha and 25 t/ha, respectively, and an OMW biochar treatment with the addition of 25 t/ha. Higher yields were observed in both SS biochar treatments, providing evidence that biochar acts as a plant bio-stimulant. Biochar application had positive impacts on carbon sequestration and soil structure. The uptake of heavy metals by all plant parts was very low, indicating that biochar is an appropriate product for land application. Biochar dose and type induced changes in the composition due to the different unique species and biodiversity of microbial communities. Venn diagrams revealed that the majority of the identified taxa were shared among the treatments, and only a small proportion of them were unique in bulk soil between treatments. In the rhizosphere, the OMW-biochar-treated plants showed a higher number of unique taxa. Microbiota structure plays a major role in the stimulation of plant growth; however, further research is needed to understand the impact of these shifts in the functioning of agroecosystems.

Sedimentary DNA for tracking the long-term changes in biodiversity

Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.

Microbial spatial distribution and corrosion evaluation in urban sewer systems with different service lives

In the present study, distribution characteristics and biodiversity of microbial communities from four real sewer pipes in urban residential area were studied. The differences of microbial community were observed in spatial distribution. The genus of Mycobacterium, Acidiphilium and Acidithiobacillus were mainly detected in the upper and middle part. Methanthrix, Longilinea and Desulfobulbus were dominant in the bottom part. Total nitrogen, sulfate and oxidation–reduction potential were identified to be the crucial driving factors in the formation of microbial community. The corrosion differences in different sites primarily resulted from the differences of microbial communities in upper parts. From the evaluation of microbial induced concrete corrosion, sulfate-reducing bacteria and fermentation bacteria in bottom part and sulfur-oxidizing bacteria in upper part played a major role. Further, the middle and end of the sewer pipes faced greater risk of concrete corrosion than the beginning parts.

The Biodiversity of Epilithic Microalgal Communities Colonising a Central Mediterranean Coastline

Schembri, S. and Zammit, G., 2022. The biodiversity of epilithic microalgal communities colonising a central Mediterranean coastline. Journal of Coastal Research, 38(2), 249–260. Coconut Creek (Florida), ISSN 0749-0208. Microbial communities colonise the coastal ecosystem around the Maltese islands. However, such communities are understudied, both in Malta and in the central Mediterranean. This research aims to increase current knowledge about the biodiversity of phototrophic communities growing along a central Mediterranean rocky shoreline and is the first such study to be performed on microorganisms growing in epilithic biofilms and microbial mats along the coastline in the Maltese islands. Samples were obtained using techniques that were noninvasive to the underlying substratum. These were studied by direct observation using light and electron microscopy, by culturing in vitro, by molecular analysis via sequencing of the small subunit ribosomal ribonucleic acid genes and phylogenetic analyses. Microscopic analyses revealed highly diverse communities made of both photosynthetic and heterotrophic organisms. The predominant microorganisms were simple filamentous cyanobacteria including species of Leptolyngbya, Phormidesmis, Nodosilinea, Toxifilum, Phormidium, and Lyngbya, as well as heterocytous Calothrix and Nunduva spp. The coccal cyanobacteria included species of Aphanocapsa and Chroococcus, whereas coccal microalgae belonged to Chlorella, Chlamydomonas, and Coelastrella spp., accompanied by diatoms of Navicula sp. These results include first records of cyanobacterial and microalgal barcodes that were genetically sequenced from a coastline in the central Mediterranean. Germlings of the filamentous macroalga Cladophora were embedded in the rocky substrate that was preconditioned by biofilm growth and ciliated protozoans, micronematodes, and microcrustaceans interacted with the microbial communities. The isolation of new cyanobacterial and microalgal strains from these phototrophic communities highlights the importance of employing a combined multiphasic approach to supplement current knowledge about the biodiversity of microbial communities colonising rocky shores.

Microbial communities reveal impacts of unconventional oil and gas development on headwater streams

The demand for natural gas has led to the development of techniques used to access unconventional oil and natural gas (UOG) resources, due to the novelty of UOG, the potential impacts to freshwater ecosystems are not fully understood. We used a dual pronged approach to study the effects of UOG development on microbial biodiversity and function via a laboratory microcosm experiment and a survey study of streams with and without UOG development within their watersheds. The microcosm experiment simulated stream contamination with produced water, a byproduct of UOG operations, using sediment collected from one high water-quality stream and two low water-quality streams. For the survey study, biofilm and sediment samples were collected from streams experiencing varying levels of UOG development. In the microcosm experiment, produced water decreased microbial aerobic and anaerobic CO2 production in the high water-quality stream sediment but had a positive effect on this microbial activity in the lower water-quality stream sediments, suggesting habitat degradation alters the response of microbes to contaminants. Results from the stream survey indicate UOG development alters stream water temperature, chemistry, sediment aerobic and anaerobic CO2 production, and microbial community biodiversity in both sediments and biofilms. Correlations among UOG associated land use, environmental, and microbial variables suggest increases in light availability and sediment delivery to streams, due to deforestation and land disturbance, impact stream microbial communities and their function. Consistent changes in the relative abundance of bacterial taxa suggest microorganisms may be good indicators of the environmental changes associated with UOG development. The observed impacts of UOG development on microbial community composition and carbon cycling could have cascading effects on stream health and broader ecosystem function.

Analysis of microbial community biodiversity in activated sludge from a petrochemical plant

Theactive sludge process is one of the most-used techniques for the biodegradation of organic compounds present in effluents from an assortment of wastewaters. This study investigated the bacterial community structure of a petroleum industry’s activated sludge and its physical and chemical parameters using high-throughput sequencing. Samples were collected over one year: autumn 2015 (C1), winter 2015 (C2), spring 2015 (C3), and summer 2016 (C4). Total DNA was extracted, and the primers targeting the V4 region of the 16S rRNA gene were used for amplicon sequencing. The majority of the detected microorganisms were considered rare microbiota, presenting a relative abundance below 1% of the total sequences. All of the sequences were classified at the phylum level, and up to 55% of the ASVs (Amplicon Sequence Variants) were associated with known bacterial genera. Proteobacteria was the most abundant phylum in three seasons, while the phylum Armatimonadota dominated in one season. The genus Hyphomicrobium was the most abundant in autumn, winter and summer, and an ASV belonging to the family Fimbriimonadaceae was the most abundant in the spring. Canonical Correspondence Analysis showed that physicochemical parameters of SS, SD and TSS are correlated, as well as ammoniacal nitrogen. Sample C3 presented the highest values of COD, AN and solids (SS, SD and TSS). The highest COD, AN, and solids values are correlated to the high frequency of the phylum Armatimonadota in C3.

Habitats and seasons differentiate the assembly of bacterial communities along a trophic gradient of freshwater lakes

Abstract Freshwater lakes are subject to variable degrees of eutrophication. Within lakes, the planktonic bacterial community (PBC) and sediment bacterial community (SBC) are both significant participants in biogeochemical processes of lake ecosystems. However, how the assembly patterns of bacterial communities vary seasonally along a trophic gradient in freshwater lakes is poorly understood. Here, we collected and analysed water and sediment samples from 13 shallow lakes located in an urban region of China during summer and winter, the trophic states of which ranged from mesotrophic to middle eutrophic in summer and oligo‐mesotrophic to light eutrophic in winter. High‐throughput sequencing of 16S ribosomal RNA genes was used to determine the diversity and composition of bacterial communities. Our results indicated that bacterial communities derived from different habitats and seasons did not exhibit a uniform response to lake trophic states. Linear and nonlinear mixed effect models suggested that the α‐diversity of PBC and SBC, respectively, showed a unimodal and monotonically decreasing trend with increasing eutrophication in summer, whereas that of PBC and SBC, respectively, exhibited no obvious trend or an increased pattern along the trophic gradient in winter. In addition, the taxonomic compositional dissimilarity of the PBC was most significantly related to lake trophic differences in summer. Phylogenetic structure analysis revealed that mostly environmental selection regulated the SBC and PBC in both seasons. Moreover, dispersal limitation and homogenising dispersal contributed more to the assembly of SBC and PBC in both seasons, respectively. Water temperature, associated with seasonal variability, was the most important variable driving the PBC assembly, while sediment pH overwhelmed nutrients in regulating the seasonal patterns of SBC assemblages. Overall, we highlighted that the water and sediments, as well as the seasons, differentiated the diversity patterns and assembly processes of bacterial communities along a trophic gradient of freshwater lakes. Our findings provide novel information for understanding the ecological responses of lacustrine bacterial communities to trophic gradients and seasonal variations. This study also contributes an important reference for predicting the changes of microbial community biodiversity under future scenarios of eutrophication. ​

Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other.

Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils—deposits collected by the epiphytes—which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.

Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea.

The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.

Microbial communities of biofilms developed in a chlorinated drinking water distribution system: A field study of antibiotic resistance and biodiversity

Antibiotic resistance and biodiversity were investigated in microbial communities attached to inner surfaces of water supply fittings in a chlorinated drinking water distribution system (DWDS) supplied by two independent water treatment plants (WTPs) drawing the same source water. The investigation of the effect of the season, the applied water treatment technology, and type, material, and age of water supply fittings on both antibiotic resistance and biodiversity in biofilms involved collection of tubercles during summer and winter seasons throughout the DWDS. A total of 16 samples were collected (8 per season) from areas supplied by two independent WTPs. Culturable aerobic antibiotic resistant bacteria (ARB) proved more prevalent in summer. Various antibiotic resistance genes (ARGs) were detected, confirming the role of biofilms as ARGs reservoirs, but the abundances of quantified genes (sulI, ermB, qacEΔ1, intI1) were low (a range of <LOQ to 2313 gene copies/mg dry mass of tubercles) throughout the DWDS. In terms of microbial community composition, Proteobacteria were dominant in each sample (51.51–97.13%), and the most abundant genus was Desulfovibrio (0.01–66.69%) belonging to sulphate-reducing bacteria. Biodiversity of microbial communities was shaped by many coexisting factors, including season, water supply fitting material, and sampling site location. Spatial distribution analysis revealed that although only samples collected at the same sampling sites were similar to each other in terms of antibiotic resistance, some samples collected in the close proximity were similar in terms of biodiversity. This suggests that antibiotic resistance spreads only locally over small distances in drinking water biofilms. Although actual drinking water biofilms have been previously investigated in terms of microbial biodiversity, this is the first study that characterised both antibiotic resistance and biodiversity of microbial communities attached to inner surfaces of a real DWDS functioning for decades.

Shotgun Metagenomic Sequencing of Extremophilic Community from Soda Lake, Ga'ar Lake, in Wadi Al-Natrun, Egypt

Shotgun metagenomic DNA sequencing is an effective ecological sequencing approach that offers understanding of microbial community biodiversity and function. This study evaluated the phylogenetic diversity and metabolic potential of the haloalkaliphilic microbial community of hypersaline and alkaline lake in Wadi Al-Natrun, Egypt, by using High-throughput sequencing technique. Metagenome comprised of 32,149,168 reads, and total read bases were 4.0G bp, with GC content 61.589% and Q30 87.847%. The brine sample of Ga’ar lake have been proceeded with library construction and revealed an enormous value for archaeal structure and functionality, the community investigation out predominance of domain Archaea (81%), including phylum Euryarchaeota, family halobacteriaceae, domain Eubacteria (2%) comprised total reads 208 OTUs of microbial community and including five phyla; Bacteraidetes (1.2%), Proteobacteria (0.3%), Firmicutes (0.1%), Chloroflexi (0.2%) and Actinobacteria (0.2%), and only 17% of total community was unassigned. In functional analysis, Gene Ontology (GO) terms derived from InterPro matches to brine sample revealed that 42% was biological processes, 52% genes for molecular functions and 6% was cellular components. Metagenomic sequence analysis indicating that this lake is promising for exploring of novel genes and extremophilic microorganisms for various purposes.

A network-based approach to deciphering a dynamic microbiome\u2019s response to a subtle perturbation

Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.

Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.

Genomic Signal Processing Techniques for Taxonomy Prediction

To analyze complex biodiversity in microbial communities, 16S rRNA marker gene sequences are often assigned to operational taxonomic units (OTUs). The abundance of methods that have been used to assign 16S rRNA marker gene sequences into OTUs brings discussions in which one is better. Suggestions on having clustering methods should be stable in which generated OTU assignments do not change as additional sequences are added to the dataset is contradicting some other researches contend that the methods should properly present the distances of sequences is more important. We add one more de novo clustering algorithm, Rolling Snowball to existing ones including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. We use GreenGenes, RDP, and SILVA 16S rRNA gene databases to show the success of the method. The highest accuracy is obtained with SILVA library.

Bacterial and archaeal taxa are reliable indicators of soil restoration across distributed calcareous grasslands

AbstractLand‐use intensification can reduce soil carbon stocks and changes microbial community biodiversity and functionality. However, there is a lack of consensus on whether management consistently affects microbial biodiversity across geographic scales, and how this relates to altered soil function. From a regulatory and monitoring perspective, there is a need to identify functionally relevant indicators of land use in order to evaluate the progress of soil restoration approaches. We performed a landscape‐scale survey of unimproved calcareous grasslands paired with local arable contrasts, and assessed the consistency of responses in a variety of soil, biotic and functional measures. In addition, adjacent grasslands undergoing restoration were assessed to identify soil microbial indicators of recovery. Organic matter content was consistently larger in grasslands than in arable fields, and increased with time in the restoring sites. Molecular comparisons of grassland versus arable soils revealed numerous bacterial, archaeal and fungal indicators, with more representatives of Ca. Xiphinematobacter, DA101, Bradyrhizobium, Rhodoplanes, Mycobacteria and Mortierella in old grassland soils, whereas Nitrososphaera, Sporosarcina and Alternaria infectoria were more abundant in arable soils. Extracellular enzymatic responses were more variable, with none of the eight investigated enzymes being consistent indicators of grassland or arable soils. Correlation analyses, incorporating the molecular and enzymatic responses across all surveyed soils, revealed that molecular indicators were more strongly correlated with soil organic matter increases with restoration of arable soils. Our results highlight that microbial taxa are among the most sensitive indicators of soil restoration, and we identify consistent responses of specific taxa to management across geographic scales. This discovery will be important for both the instigation and monitoring of soil restoration.Highlights Soil microbes are key drivers of soil ecosystem services and are affected by management Calcareous grassland exhibited abundant Verrucomicrobia; cropping increased Nitrososphaera These taxa responded to SOM increases with grassland restoration, more so than enzymes and fungi Microbes provide consistent, site‐independent indicators for calcareous grassland soil function restoration

Nanofiltration in pilot scale for wastewater reclamation: Long-term performance and membrane biofouling characteristics

Nanofiltration (NF) has been recognized as a cost-effective membrane technology for wastewater reclamation, while little information is available about its performance in pilot scale for practical engineering application. In addition, the biofouling issue is always a barrier to membrane process for its long-term stable operation which requires further investigations. In this study, the performance of a pilot-scale two-stage NF system was continually monitored for three months. The membrane autopsy characterization was conducted when the irreversible membrane fouling occurred. The rejections of COD, TOC and TP by NF were 96.5 ± 1.2%, 91.9 ± 1.9% and 97.7 ± 2.1%, respectively. A total of 23 emerging contaminants have been detected in NF influent, including 19 pharmaceuticals and personal care products (PPCPs) and four environmental estrogens (EEs). Except for bisphenol A (57.6%) and ibuprofen (69.9%), the rejections of other 21 emerging contaminants were all higher than 80% by the NF system. Microbial community structure analysis showed that Proteobacteria and Bacteroidetes were the two predominant bacteria on the membrane surface with percentages of 34.1%-41.0% and 23.4%-30.6% at phylum level, respectively. At genus level, Stenotrophomonas and Pseudoxanthomonas were primarily dominant in the first stage, while Cloacibacterium and Methyloversatilis showed higher relative abundances in the second stage. Sphingopyxis was an extremely stubborn genus on the membrane surface. Besides, the biodiversity of microbial communities in the first stage was higher than that in the second stage, possibly showing more severe biofouling in the first stage of the two-stage NF system. This study has provided insights to understand the practical performance of NF technology in pilot scale and could give guideline for biofouling control in NF engineering application.

Rice waste biochars produced at different pyrolysis temperatures for arsenic and cadmium abatement and detoxification in sediment

The effectiveness of rice waste biochars on heavy metal and metalloid abatement and detoxification was investigated using comprehensive studies based on As and Cd immobilization, bioaccumulation in tubifex, and microbial community changes in contaminated sediment. The remediation effects of biochars produced at different pyrolytic temperatures (400–700 °C) were evaluated. Bioaccumulation of heavy metal and metalloid in the tubifex tissue and change of indigenous microbial community under treatment of different biochars were assessed. Biochars produced at 700 °C exhibited greater effect on decreasing the concentrations of As and Cd in aqueous phase, and TCLP extractable and bioavailable metal(loid) in solid phase of sediment. The concentration of As and Cd in water phase decreased by 26%–89% and 22%–71% under the treatment of straw biochar, and decreased by 13%–92% and 5%–64% under the treatment of rice husk biochar, respectively. As and Cd contents in the tubifex tissue were positively correlated with their concentrations in aqueous phase. High-temperature biochars significantly reduced metal(loid) bioaccumulation in tubifex. The richness and biodiversity of microbial community were both greater in all biochars remediated sediment compared to non-treated sediment. These results indicated that rice waste biochars could effectively inhibit the bio-availability and toxicity of heavy metal and metalloid in sediment, and the higher-temperature biochar exhibited better performance.

Biodiversity of microbial communities on some species in the class Gastropoda common in coastal waters in Central Vietnam

Gastropoda is a large class in coastal waters in Central Vietnam. The interaction between microorganisms and Gastropoda mainly consists of symbiotic and parasitic relationships. In this study, biodiversity of microbial communities on some species of Gastropoda is evaluated, thereby predicting their interaction. From 12 samples of Gastropoda including 3 species: Trochus maculatus , Cypraea eglantica , Chicoreus bruneus , 101 microorganism strains including 79 bacterial strains (78.2%), 18 yeast strains (17.8%) and 4 actinomycetes strains (4.0%) were isolated. There were 15 strains (including 8 yeast strains, 5 bacterial strains and 2 actinomycetes strains) selected to identify based on sequence analysis of the D1/D2 region (yeast) and 16S rRNA gene (bacteria and actinomycetes). Based on the identification results, it is possible to predict the nutritional relationship between microorganisms and species of Gastropoda.

Bacterial Communities of Microbial Mats of the White Sea Supralittoral and of the Littoral of the Lakes Separated from the Sea

Conditions of formation and phylogenetic composition were studied for pigmented biofilms and microbial mats of the Kandalaksha Bay (White Sea) supralittoral and of the littoral of the lakes separated from the sea. During the sampling period, salinity was 15 to 26 g/L, except for several desalinated salt marsh sites (4‒11 g/L); the temperature was 9‒12°C. The species composition and structure of benthic phototrophic communities were affected by severe climatic conditions of the area, including low average annual temperature and freezing of the littoral zones. Application of Next-generation sequencing of the 16S rRNA gene V3-V4 regions combined with microscopy of the samples and obtained cultures for analysis of the biodiversity of microbial communities resulted in improved understanding of diversity of both oxygenic and anoxygenic bacteria in the Kandalaksha Bay littoral. No significant differences were revealed in species composition of microbial mats from salt marshes and shallow sites of the lakes of marine origin. Members of the phyla Bacteroidetes (up to 36%) and Proteobacteria (up to 67%) predominated in the mats and biofilms. The share of phototrophic bacteria was 0.3–18%. Oxygenic phototrophs (cyanobacteria Phormidium, Oscillatoria, Spirulina, and Anabaena, as well as diatoms) predominated in the phototrophic community. The species number of anoxygenic phototrophic bacteria did not exceed 5% of all prokaryotes. These were mainly mesophilic marine species of purple sulfur bacteria of the genera Thiorhodococcus and Thiocapsa. No members of the family Ectothiorhodospiraceae, which are typical of microbial mats from southern seas, were found in subpolar microbial mats. Nonsulfur purple bacteria and aerobic anoxygenic phototrophic bacteria were mostly similar to the known marine species. Green sulfur bacteria (salt-water Prosthecochloris and Сhlorobium species) were detected in two coastal mat samples from meromictic lakes. Anoxygenic filamentous phototrophic bacteria, which occurred in almost all benthic phototrophic communities, were represented by new phylotypes.

Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.

Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.