Prokaryotic Community Structure Research Articles

Spatial abundance distribution of prokaryotes is associated with dissolved organic matter composition and ecosystem function

AbstractDiverse prokaryotic communities consume and transform a broad suite of molecules in the dissolved organic matter (DOM) pool, which controls major biogeochemical cycles. Despite methodological advancements that provide increasingly more detailed information on the diversity of both prokaryotic communities and DOM components, understanding how these two component parts are structured to influence ecosystem functioning remains a major challenge in microbial ecology. Using empirical data collected along a gradient of productivity in the Labrador Sea, we characterized relationships among DOM compounds, metabolic processing, and prokaryotic diversity by structuring prokaryotic communities using spatial abundance distribution (SpAD) modeling. We identified strong associations of different SpAD taxonomic groups with specific organic substrates as well as with metabolic rates. Amplicon sequence variants (ASVs) with more cosmopolitan distributions (i.e. normal‐like) such as Bacteroidia were related to fresher DOM substrates such as free and combined amino acids whereas rare ASVs (i.e. logistic) like δ‐proteobacteria were associated with complex forms of organic matter. In terms of ecosystem function, rates of respiration and production were most strongly predicted by the abundance of certain SpAD taxonomic groups. Given the importance and complexity of linking environmental conditions, prokaryotic community structure, and ecosystem function, we propose a framework to bridge the gap between prokaryotic diversity, microbial ecology, and biogeochemistry among methods and across scales. Our work suggests that SpAD modeling can be used as an intermediate step to link prokaryotic community structure to both finer DOM details and larger ecosystem scale processes.

Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient.

Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.

Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities.

Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.

Prokaryotic communities of technozems of the spoil heaps of Kursk magnetic anomaly

Background. Spoil heaps chronosequences are convenient models to analyze the succession of microbiome during restoration of anthropogenically disturbed landscapes. The investigation of the heavy metal content in lands with mining activity, can be used as an indicator of ecosystem recovery.
 Materials and methods. Objects were technozems of 1-year, 25- and 50-year-old embryonic soils, and control soil under forest. Quantitative polymerase chain reaction (qPCR) and NGS-sequencing of V4 region of 16S rRNA gene were applied. Results. During the soil-forming process, an increase organic carbon and nitrogen, as well as a gradual increase archaeal 16S rRNA gene copies and in the number of Bradyrhizobiaceae, Blastocatellaceae, Xantobacteriaceae. Although we found a number of taxa that increased during soil-forming process (Thaumarchaeota, Bradyrhizobiaceae, Blastocatellaceae, Xantobacteriaceae), technozems of different ages had a similar structure and diversity of prokaryotic communities, differing from a nature soil. Biodiversity analysis revealed that technozems generally had a similar structure and diversity of prokaryotic communities, significantly differing from the mature soil a specific clusterization of microbiomes. The HM contents and bacterial abundances remained at the same level in chronosequence.
 Conclusions. The 50 years of soil development on overburden spoil heaps is not enough for the recovery from HM contamination and restoration of soil ecosystem functioning.

Profiling the composition and metabolic activities of microbial community in fermented grain for the Chinese strong-flavor Baijiu production by using the metatranscriptome, high-throughput 16S rRNA and ITS gene sequencings

The composition and function of microbial community analyzed by sequencing 16S rRNA/ITS gene amplicons (DNA level) were compared with those derived by using metatranscriptome sequencing (RNA level) from the same fermented grain (FG) sample, which obtained from the key fermentation time point during the Chinese strong-flavor Baijiu (CSFB) production process. The results showed that the fungi with the highest relative abundance was Saccharomyces (RNA: 83.15%, DNA: 89.74%) at the two levels. The most abundant bacterium was Kroppenstedtia (37.09%) detected only at the DNA level, while it was Streptococcus (93.75%) at the RNA level, indicating that the structures of prokaryotic communities at the two levels were quite different. For the microbial functions, a large proportion of genes of FG microorganisms related to “Metabolism” function were observed both by using PICRUSt2 analysis (DNA level) and metatranscriptome analysis (RNA level), and especially enriched in “Carbohydrate metabolism”. While the proportions of genes involved in some functions were different, such as “Replication and repair”, “Membrane transport” and “Environmental adaptation”, with high proportions of genes involved in at the DNA level when compared those at the RNA level. Furthermore, Saccharomyces cerevisiae was the most active microbe in the top15 pathways, followed by Torulaspora dellbrueckii. During the conversion of starch to ethanol, S. cerevisiae showed high metabolic capacity, and cooperated with other microorganisms to convert pyruvate to acetaldehyde directly or through acetyl-CoA and acetate, and then acetaldehyde to ethanol. As far as we know, this is a first study to profile the microbial community and metabolic features in FG of CSFB by using a combination of DNA- and RNA- based technologies. Our findings could provide useful insights for further understanding the active microbial function, metabolic pathways and fermentation mechanism in the FG ecosystem during CSFB fermentation.

Changes in soil prokaryotic community structure following pesticide additions to agrosoddy-podzolic soil

The microbial community is an essential component of the soil ecosystem. The application of mineral fertilizers and pesticides leads to taxonomic and functional rearrangements in the structure of the prokaryotic soil community. Compared with classical cultivation methods, molecular genetic techniques of analysis make it possible to estimate the extent of these changes with a given accuracy. The aim of the work was to study the effect of three pesticides on the structure of the prokaryotic community of agrosoddy-podzolic soil using DNA metabarcoding and metagenomics. With the joint application of three pesticides, the dominance of representatives of the phylogenetic group Proteobacteria is observed in the soil microbial community. When the herbicide of metribuzin is applied to the soil at a 10-fold rate, the proportion of bacteria Flavisolibacter ginsengisoli increases. It was found that when the herbicide, insecticide and fungicide are applied individually, the bacteria are reduced in the number of Mycobacterium madagascariense and Candidatus Nitrocosmicus bacteria. In all variants of the experiment, when pesticides were added, both in the recommended application rate and in the 10-fold rate, an increase in the presence of bacteria Sphingomonas parvus was observed. This indicates a high hydrolytic activity of these bacteria. The established fact can be used in further experiments on the pesticide biodegradation and on the remediation of contaminated areas.

Environmental Atlas of Prokaryotes Enables Powerful and Intuitive Habitat-Based Analysis of Community Structures.

SummaryThe recent prevalence of high-throughput sequencing has been producing numerous prokaryotic community structure datasets. Although the trait-based approach is useful to interpret those datasets from ecological perspectives, available trait information is biased toward culturable prokaryotes, especially those of clinical and public health relevance, and thus may not represent the breadth of microbiota found across many of Earth's environments. To facilitate habitat-based analysis free of such bias, here we report a ready-to-use prokaryotic habitat database, ProkAtlas. ProkAtlas comprehensively links 16S rRNA gene sequences to prokaryotic habitats, using public shotgun metagenome datasets. We also developed a computational pipeline for habitat-based analysis of given prokaryotic community structures. After confirmation of the method effectiveness using 16S rRNA gene sequence datasets from individual genomes and the Earth Microbiome Project, we showed its validness and effectiveness in drawing ecological insights by applying it to six empirical prokaryotic community datasets from soil, aquatic, and human gut samples.

Occurrence and role of virioplankton in a tropical estuarine system

Only a few studies have reported on viral dynamics in estuarine environments, and the factors regulating viral ecology are not well known. We herein aimed to address the factors controlling virus–host relationships in tropical estuaries. To accomplish this, we combine a historical data series (2011–2017), containing virus and prokaryote abundances, with environmental data from Guanabara Bay, Brazil. Water quality gradients and tides were found to regulate the structure of prokaryotic communities, and seasonal patterns added complexity to the dynamics of viral populations. Prediction models showed a balance between expected and recorded virus–host relationships. However, changes in virus-microbial ratio (VMR) were found in areas with microorganism increases and regions showing critical environmental changes. Our results demonstrated that VMR changes are multifactorial and cannot be associated with any specific factor. Neither Kill-the-Winner nor Piggyback-the-Winner models can predict VMR in a highly dynamic environment strongly influenced by eutrophication. In sum, it can be concluded that special care is necessary when analyzing models for predicting virus and host abundances, as ecological factors control host distribution and play a significant role in the virus–host relationship.

Comparison of Prokaryotic Communities Associated with Different TOC Concentrations in Dianchi Lake

The effect of total organic carbon (TOC) on the prokaryotic community structure in situ has been rarely known. This study aimed to determine the effect of TOC level on the composition and networks of archaeal and bacterial communities in the sediments of Dianchi Lake, one of the most eutrophic lakes in China. Microbial assemblages showed significantly associations with TOC. Moreover, relatively high and low TOC formed taxonomic differences in prokaryotic assemblages. According to the results, the most abundant bacteria across all samples were identified as members of the phyla Proteobacteria, Nitrospirae, Chloroflexi, Firmicutes and Ignavibacteriae. The dominant groups of archaea consisted of Euryarchaeota, Woesearchaeota DHVEG-6, Bathyarchaeota and WSA2. Lastly, the meta-analysis results highlighted that the low TOC (LT) prokaryotic community structure is larger and more complex compared to moderate TOC (MT). On the whole, the prokaryotic community structure is obviously distinct among groups with different TOC levels, and LT communities may interact with each other strongly in the Dianchi Lake sediment. This study can provide more insights into prokaryotic assemblages in eutrophic lake sediment and provide suggestions for the restoration and maintenance of sediment ecosystems.

Insight into the hidden bacterial diversity of Lake Balaton, Hungary

In the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum beta-lactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.

Rewilding the small stuff: the effect of ecological restoration on prokaryotic communities of peatland soils

To investigate the effect that restoration has on the microbiome of wetland soils, we used 16S amplicon sequencing to characterize the soil prokaryotic communities of retired cranberry farms that were restored to approximate the peat wetlands they once were. For comparison, we also surveyed the soil communities of active cranberry farms, retired cranberry farms and natural peat wetlands that were never farmed. Our results show that the prokaryotic communities of active cranberry farms are distinct from those of natural peat wetlands. Moreover, 4 years after restoration, the prokaryotic community structure of restored cranberry farms had shifted, resulting in a community more similar to natural peat wetlands than to active farms. Meanwhile, the prokaryotic communities of retired cranberry farms remained similar to those of active farms. The observed differences in community structure across site types corresponded with significant differences in inferred capacity for denitrification, methanotrophy and methanogenesis, and community composition was also correlated with previously published patterns of denitrification and carbon sequestration measured from the same soil samples. Taken together, these results suggest that ecological restoration efforts have the potential to restore ecosystem functions of soils and that they do so by 'rewilding' the communities of resident soil microbes.

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya.

Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial populations. In this study, we investigated the effect of conventional versus organic farming systems at low and high input levels on structure and diversity of prokaryotic microbial communities. Soil samples were collected from the ongoing long-term farming system comparison trials established in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample were analyzed. Total DNA and RNA amplicons of variable region (V4-V7) of the 16S rRNA gene were generated on an Illumina platform using the manufacturer's instructions. Diversity indices and statistical analysis were done using QIIME2 and R packages, respectively. A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97% genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely, while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria and Acidobacteria. Conventional farming systems showed a higher species richness and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets were similar. Physiochemical factors were associated differently depending on rRNA and rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc, iron, boron and micro-aggregates showed a significant influence on the observed microbial diversity. The observed higher species diversity in the conventional farming systems can be attributed to the integration of synthetic and organic agricultural inputs. These results show that the type of inputs used in a farming system not only affect the soil chemistry but also the microbial population dynamics and eventually the functional roles of these microbes.

Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles.

Microbes associated with sinking marine particles play key roles in carbon sequestration in the ocean. The sampling of particle-attached microorganisms is often done with sediment traps or by filtration of water collected with oceanographic bottles, both involving a certain time lapse between collection and processing of samples that may result in changes in particle-attached microbial communities. Conversely, in situ water filtration through submersible pumps allows a faster storage of sampled particles, but it has rarely been used to study the associated microbial communities and has never been compared to other particle-sampling methods in terms of the recovery of particle microbial diversity. Here we compared the prokaryotic communities attached to small (1–53 μm) and large (>53 μm) particles collected from the mesopelagic zone (100–300 m) of two Antarctic polynyas using in situ pumps (ISP) and oceanographic bottles (BTL). Each sampling method retrieved largely different particle-attached communities, suggesting that they capture different kinds of particles. These device-driven differences were greater for large particles than for small particles. Overall, the ISP recovered 1.5- to 3-fold more particle-attached bacterial taxa than the BTL, and different taxonomic groups were preferentially recovered by each method. In particular, typical particle-attached groups such as Planctomycetes and Deltaproteobacteria recovered with ISP were nearly absent from BTL samples. Our results suggest that the method used to sample marine particles has a strong influence in our view of their associated microbial communities.

Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils.

As reported in many aquatic environments, recent studies in terrestrial ecosystems implicate a role for viruses in shaping the structure, function, and evolution of prokaryotic soil communities. However, given the heterogeneity of soil and the physical constraints (i.e., pore-scale hydrology and solid-phase adsorption of phage and host cells) on the mobility of viruses and bacteria, phage-host interactions likely differ from those in aquatic systems. In this study, temporal changes in the population dynamics of viruses and bacteria in soils under different land management practices were examined. The results showed that bacterial abundance was significantly and positively correlated to both virus and inducible prophage abundance. Bacterial and viral abundance were also correlated with soil organic carbon and nitrogen content as well as with C:N ratio. The seasonal variability in viral abundance increased with soil organic carbon content. The prokaryotic community structure was influenced more by land use than by seasonal variation though considerable variation was evident in the early plant successional and grassland sites. The free extracellular viral communities were also separated by land use, and the forest soil viral assemblage exhibiting the most seasonal variability was more distinct from the other sites. Viral assemblages from the agricultural soils exhibited the least seasonal variability. Similar patterns were observed for inducible prophage viral assemblages. Seasonal variability of viral assemblages was greater in mitomycin-C (mitC) induced prophages than in extracellular viruses irrespective of land use and management. Taken together, the data suggest that soil viral production and decay are likely balanced but there was clear evidence that the structure of viral assemblages is influenced by land use and by season.

Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters.

Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L–1) and intense (10 μg of Chlorophyll a L–1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes’ abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.

Prokaryotic Capability to Use Organic Substrates Across the Global Tropical and Subtropical Ocean.

Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 plates® in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean.

Shifting prokaryotic communities along a soil formation chronosequence and across soil horizons in a South Taiga ecosystem

The study of chronosequences allows the analysis of the temporal and spatial dynamics of ecogenesis, soil microbiome and soil development. Here, we investigated the taxonomic diversity of bacterial and archaeal communities along a chronosequence of soils that formed on four Lake Ladoga coastal bars in the Nizhnesvirsky Nature Reserve (Leningrad region, north-west Russian Federation). We analyzed two factors: the age of sampled solum (ranging from 70 to 1,590 years) and the soil horizons that differ in terms of morphology and genesis.We observed a relationship between podzolisation, typical major soil-forming processes of the southern taiga zone, and the taxonomic structure of prokaryotic communities. The most pronounced differences between microbial communities were associated with the vertical heterogeneity of soil profile. Phyla associated with copiotrophic habits (Proteobacteria, Actinobacteria and Bacteroidetes) were more frequent in topsoil. Podzolic eluvial (E) horizons had higher frequencies of the genus Mycobacterium (Actinobacteria). In deeper horizons, we observed lower frequencies of copiotrophic phyla and increased frequencies of phyla associated with oligotrophic habits (Nitrospirae, Gemmatomonadetes, Planctomycetes, Chloroflexi, etc.), as well as archaeal lineages. The lowest (gleyic, G) horizons had high frequencies of anaerobic and methane-producing bacteria.Therefore, the relationship between microbial community structure and the continuous development of the soil profile was revealed. Shifting physico-chemical were identified as key factors associated with variation in prokaryotic communities. The older coastal bar demonstrated the clearer signs of podzol formation, increased thickness of the E horizon, and increased differentiation among microbial communities in different genetic horizons.

Functional and Structural Responses of Arctic and Alpine Soil Prokaryotic and Fungal Communities Under Freeze-Thaw Cycles of Different Frequencies.

Ongoing climate change involves increasing snow scarcity, which results in more frequent freeze-thaw cycles (FTCs) in polar and alpine soils. Although repeated FTCs have been shown to alter the structure and functions of soil microbial communities, a thorough understanding on the influence of FTCs frequency on polar and especially alpine soil microbiomes is still elusive. Here, we investigated the impact of repeated weekly vs. daily FTC frequencies on the structure and functions of prokaryotic and fungal communities from north- and south-exposed soils from two mountain ridges, one in the Arctic and one in the High-Alps. FTCs affected prokaryotic communities more strongly than fungal communities, where mainly cold-tolerant and opportunistic fungi (e.g., Mrakia, Mortierella) were responsive. Prokaryotic communities were more affected by weekly FTCs than by daily FTCs. Daily FTCs favored fast-growing bacteria (e.g., Arthrobacter), while oligotrophic and largely uncultured taxa (e.g., Verrucomicrobia) benefited from weekly FTCs. FTCs negatively affected microbial respiration but had minor impacts on C-, N- and P-acquiring enzymatic activities. Plausible pre-adaptation of the microbial communities to naturally occurring frequent FTCs at their site of origin did not show a clear influence on the microbial responses to the tested FTCs. Altogether, our study provides an integrative overview on potential structural and functional changes of soil microbial communities in polar and alpine regions in response to the projected increase in FTCs; therefore advancing our understanding on the impact of climate change in these rapidly changing ecosystems.

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities

The widespread use of levofloxacin (LEV) and oxytetracycline (OTC) in hospitals and farms inevitably contributes to water pollution through waste disposal processes, municipal wastewater treatment, and manure application to farmlands, which adversely affects aquatic microorganisms. Here, we evaluated the toxicity of LEV and OTC to cyanobacteria and eukaryotic algae monocultures and freshwater microcosms. Three test cyanobacteria were inhibited by both LEV and OTC at all examined concentrations. The growth of the eukaryotic organisms C. vulgaris and Monoraphidium sp. was only inhibited by high concentrations of OTC ranging from 1000 to 10,000 μg/L; however, they were less sensitive to LEV and OTC than cyanobacteria. In the aquatic microcosms, 5 μg/L of LEV and OTC did not affect the alpha diversity of prokaryotic and eukaryotic communities or the composition of the eukaryotic microbial communities after 14 d of exposure. However, this concentration of LEV and OTC significantly changed the prokaryotic microbial community structure at the genus level, and different antibiotics affected the prokaryotic microbial community differently, suggesting that different antibiotics affect prokaryotes through different molecular mechanisms, thereby leading to differences in prokaryotic microbial growth patterns. Moreover, the changes in the prokaryotic microbial community composition suggested that low antibiotic concentrations in water could disturb prokaryotic microbial communities and cause ecological risks.

Characterization of Microbial Diversity and Community Structure in Fermentation Pit Mud of Different Ages for Production of Strong-Aroma Baijiu.

In the traditional fermentation process of strong-aroma Baijiu, a fermentation pit mud (FPM) provides many genera of microorganisms for fermentation. However, the functional microorganisms that have an important effect on the quality of Baijiu and their changes with the age of fermentation pit (FP) are poorly understood. Herein, the Roche 454 pyrosequencing technique and a phospholipid fatty-acid analysis were employed to reveal the structure and diversity of prokaryotic communities in FPM samples that have been aged for 5, 30, and 100 years. The results revealed an increase in total prokaryotic biomass with an FP age; however, Shannon’s diversity index decreased significantly (p < 0.01). These results suggested that a unique microbial community structure evolved with uninterrupted use of the FP. The number of functional microorganisms, which could produce the flavor compounds of strong-aroma Baijiu, increased with the FP age. Among them, Clostridium and Ruminococcaceae are microorganisms that directly produce caproic acid. The increase of their relative abundance in the FPM might have improved the quality of strong-aroma Baijiu. Syntrophomonas, Methanobacterium, and Methanocorpusculum might also be beneficial to caproic acid production. They are not directly involved but provide possible environmental factors for caproic acid production. Overall, our study results indicated that an uninterrupted use of the FP shapes the particular microbial community structure in the FPM. This research provides scientific support for the concept that the aged FP yields a high-quality Baijiu.