Prokaryotic Community Composition Research Articles

Prokaryotic Community Compositions of the Hypersaline Sediments of Tuz Lake Demonstrated by Cloning and High-Throughput Sequencing

Tuz Lake is a shallow, perennial, inland hypersaline lake located at the center of the Turkey. Microbial populations developing in the sedimentary layers of the lake were investigated by using 16S rRNA gene-targeted Illumina MiSeq sequencing and cloning. A total of 11 samples were taken from three sampling points. Here we report the relative abundance of microbial taxa distributed across the sediment samples. Abundant, rare and region-specific prokaryotic taxa were also examined and compared. The majority of high-throughput sequences were associated with the classes Halobacteria, Gammaproteobacteria, Bipolaricaulia, Desulfovibrionia, candidate division MSBL-1, Bacteroidia, and Desulfobacteria. Gemmatimonadota_c, Rhodothermia, Alphaproteobacteria, Methanonatronarchaeia, Thermoplasmata, Halanaerobiia, Desulfobulbia, and Bacilli were other notable taxa with low abundance. A genus belonging to Bipolaricaulia was the most abundant taxon, accounting for 11.5% of all MiSeq reads. Reads affiliated with the genera Halomonas, Desulfovermiculus, MSBL-1_g1, and Halodesulfurarchaeum were also detected at high abundance. Bipolaricaulota, Bacteroidales, Desulfosalsimonas, Desulfobulbales, Gemmatimonadota, Lentisphaeria, Halobacteriales, MSBL-1, Thermoplasmata, and DHVEG-1 related phylotypes were also frequently represented in the clone libraries.

Differences in Tetracycline Antibiotic Resistance Genes and Microbial Community Structure During Aerobic Composting and Anaerobic Digestion.

Antibiotics are widely added to swine forage and are the main reason for the environmental accumulation of antibiotic resistance genes (ARGs) in swine manure-dwelling microorganisms. Aerobic composting (AC) and anaerobic digestion (AD) are efficient methods for converting swine manure to bio-fertilizer while degrading residual antibiotics. However, the influence of these methods on ARG accumulation and the difference in their efficiency have rarely been investigated. In this study, we explored the variations in four tetracycline antibiotics (TCs) and their associated ARGs and in microbial communities after AC and AD treatment. After full-scale manure AC and AD, the four TCs were removed effectively. AD had a higher TC removal efficiency than AC and a slower rate of TC-associated ARG accumulation. In addition, the community structure was more stable in the AC and AD manures than in untreated manure, and the relationship among microbial species also evolved into competition from mutualism after both AC and AD treatment. It was also speculated that the genera Acholeplasma and Arthrobacter were the possible hosts of tetO, tetW, and tetQ; the shift in the prokaryotic community composition and the alleviation of selective pressure by TC degradation led to decreased relative abundance of ARGs in AD- and AC-treated manure.

Increasing the Sustainability of Maize Grain Production by Using Arbuscular Mycorrhizal Fungi Does Not Affect the Rumen of Dairy Cattle (Bos taurus) and Buffalo (Bubalus bubalis).

New approaches are needed to improve the sustainability of feed production and utilization by ruminants. Promising approaches include increased use of buffaloes for more sustainable milk production, and arbuscular mycorrhizal fungi (AMF) to reduce crop production input needs. However, studies assessing the effect of crops grown in the presence of AMF on rumen microbial utilization are limited. Based on current knowledge, we hypothesized that maize grain grown on AMF-inoculated soil affected ruminal fermentation and microbiota, and that this effect differed between buffalo and cattle. A dietary cross-over study (four weeks per diet) was conducted using rumen-cannulated cattle (n = 5) and buffalo (n = 6) to assess the effect of maize grain (3.9% (w/v) of diet) grown on soil with or without AMF (15 kg/ha) on ruminal fermentation and microbiota. Production of maize on AMF-treated soil did not affect any of the assessed ruminal fermentation parameters, microbial concentrations, or prokaryotic community composition (using prokaryotic 16S rRNA gene sequence analysis). In contrast, host type had numerous effects. Protozoal counts, lactate, total VFA and isobutyrate, were significantly higher in buffaloes compared to cattle. Conversely, butyrate was significantly lower in buffaloes than in cattle. Host type explained 9.3% of the total variation in prokaryotic community composition, and relative abundance of nine amplicon sequence variants significantly differed between host types. These findings indicate that AMF treatment of maize crops has no detrimental impact on the value of the resulting maize grains as a ruminant feed, and provides additional insight into rumen-based differences between cattle and buffalo.

Effects of nitrogen and phosphorus addition on microbial community composition and element cycling in a grassland soil

Microorganisms mediate nutrient cycling in soils, and thus it is assumed that they largely control responses of terrestrial ecosystems to anthropogenic nutrient inputs. Therefore, it is important to understand how increased nitrogen (N) and phosphorus (P) availabilities, first, affect soil prokaryotic and fungal community composition and second, if and how changes in the community composition affect soil element cycling. We measured soil microbial communities and soil element cycling processes along a nine-year old experimental N-addition gradient partially crossed with a P-addition treatment in a temperate grassland. Nitrogen addition affected microbial community composition, and prokaryotic communities were less sensitive to N addition than fungal communities. P addition only marginally affected microbial community composition, indicating that P is less selective than N for microbial taxa in this grassland. Soil pH and total organic carbon (C) concentration were the main factors associated with prokaryotic community composition, while the dissolved organic C-to-dissolved N ratio was the predominant driver of fungal community composition. Against our expectation, plant biomass and plant community structure only explained a small proportion of the microbial community composition. Although microbial community composition changed with nutrient addition, microbial biomass concentrations and respiration rates did not change, indicating functional redundancy of the microbial community. Microbial respiration, net N mineralization, and non-symbiotic N2 fixation were more strongly controlled by abiotic factors than by plant biomass, plant community structure or microbial community, showing that community shifts under increasing nutrient inputs may not necessarily be reflected in element cycling rates. This study suggests that atmospheric N deposition may impact the composition of fungi more than of prokaryotes and that nutrient inputs act directly on element-cycling rates as opposed to being mediated through shifts in plant or microbial community composition.

Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler.

The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.

Chloroflexi Dominate the Deep-Sea Golf Ball Sponges Craniella zetlandica and Craniella infrequens Throughout Different Life Stages

Deep-sea sponge grounds are underexplored ecosystems that provide numerous goods and services to the functioning of the deep-sea. This study assessed the prokaryotic diversity in embryos, juveniles and adults of Craniella zetlandica and Craniella infrequens, common and abundant representatives of deep-sea sponge grounds in the North Atlantic. Our results reveal that symbiont transmission in Craniella sponges likely occurs vertically, as highly similar microbial consortia have been identified in adults, embryos, and juvenile stages. Moreover, transmission electron microscopy revealed high abundances of sponge-associated microorganisms, among which Chloroflexi (SAR 202) were identified as common representatives by amplicon sequencing and fluorescent in-situ hybridization (FISH). Equal diversity metrices, a similar overall prokaryotic community composition and a distinct dominance of the phylum Chloroflexi within all life stages are the key findings of our analyses. Information such as presented here provide understanding on the recruitment of deep-sea sponge holobionts which is needed to develop integrated management tools of such vulnerable marine ecosystems.

Prokaryotic community composition in a great shallow soda lake covered by large reed stands (Neusiedler See/Lake Fertő) as revealed by cultivation- and DNA-based analyses.

Little is known about the detailed community composition of heterotrophic bacterioplankton in macrophyte-dominated littoral systems, where a considerable amount of dissolved organic carbon originates from aquatic macrophytes instead of phytoplankton. The aim of the present study was to reveal the effect of macrophytes on the microbial community and to elucidate their role in a macrophyte-dominated shallow soda lake, which can be characterised by a mosaic of open waters and reed marsh. Therefore, 16S rRNA gene amplicon sequencing, the most probable number method, cultivation of bacterial strains, EcoPlate and cultivation-based substrate utilisation techniques were applied. Differences in the structures of microbial communities were detected between the water and the sediment samples and between vegetated and unvegetated water samples. Planktonic bacterial communities of an inner pond and a reed-covered area showed significant similarities to each other. Woesearchaeia was the dominant archaeal taxon in the water samples, while Bathyarchaeia, 'Marine Benthic Group D' and 'DHVEG-1' were abundant in the sediment samples. The most probable number of heterotrophic bacteria was lower in the open water than in the reed-associated areas. The vast majority (83%) of the isolated bacterial strains from the water samples of the reed-covered area were able to grow on a medium containing reed extract as the sole source of carbon.

Seasonal Niche Partitioning of Surface Temperate Open Ocean Prokaryotic Communities.

Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche.

Depression of soil nitrogen fixation by drying soil in a degraded alpine peatland

Soil biological nitrogen fixation (BNF) represents a major pathway through which nitrogen enters pristine peatlands. Many peatlands have been undergoing human-induced changes in environmental factors, while environmental changes dramatically affect the community composition and activity of nitrogen-fixing prokaryotes (i.e., diazotrophs). However, the impact of peatland degradation on soil BNF remains unclear. By carrying out a field campaign, we examined how soil BNF varies along a natural gradient from pristine marshes to moderately-degraded meadows and sandy meadows on the Zoige Plateau. Plant and topsoil samples from four pristine marshes, three moderately-degraded meadows, and three sandy meadows were collected to determine the potential rate of nitrogen fixation (RNfix), abundance of the nifH gene, diazotrophic community composition, and soil and plant characteristics. Our results showed that topsoil RNfix varied in the range 0.018–3.00 μmol N g d.w.−1 day−1 (i.e. 21.74–1632.37 mg N m−2 day−1) across the ten sites, being lowest in sandy meadows and highest in pristine marshes. Topsoil RNfix and diazotrophic abundance were positively correlated with soil water content, sedge cover, plant biomass, soil organic carbon content, and total nitrogen and phosphorus contents. Soil water content, which affected most plant and soil characteristics, had dominant influences on the abundance and community structure of diazotrophs. The RNfix was closely correlated with the abundance of dominant diazotroph groups. The community composition of diazotrophs differed markedly among sites of different degradation levels. Proteobacteria was the most abundant diazotrophic phylum across the ten sites. Heterotrophic diazotrophs acted as the major contributor to BNF, especially in pristine marshes and moderately-degraded meadows. We conclude that soil water content was the main factor driving the depressed soil BNF during peatland degradation in Zoige, due to soil water effects on plant cover and biomass, soil organic carbon and total phosphorus, and the abundance and community structure of diazotrophs.

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC).

Plant based by-products (BP) produced from food and bioethanol industries are human inedible, but can be recycled into the global food chain by ruminant livestock. However, limited data is available on the methanogenesis potential associated with supplementing a solely BP formulated concentrate to a pastoral based diet. Therefore the objective of this in vitro study was to investigate the effects of BP inclusion rate (in a formulated concentrate) to a pasture based diet on dietary digestibility, rumen fermentation patterns, methane production and the prokaryotic microbial community composition. Diets consisted of perennial ryegrass and one of two supplementary concentrates, formulated to be isonitrogenous (16% CP) and isoenergetic (12.0 MJ/ME/kg), containing either 35% BP, barley and soybean meal (BP35) or 95% BP (BP95) offered on a 50:50 basis, however, starch, NDF and fat content varied. The BPs, included in equal proportions on a DM basis, were soyhulls, palm kernel expeller and maize dried distillers grains. The BP35 diet had greater (P < 0.05) digestibility of the chemical constituents DM, OM, CP, NDF, ADF. Greater total VFA production was seen in the BP35 diet (P < 0.05). Daily methane production (mmol/day; +22.7%) and methane output per unit of total organic matter digested (MPOMD; +20.8%) were greatest in the BP35 diet (P < 0.01). Dietary treatment influenced microbial composition (PERMANOVA; P = 0.023) with a greater relative abundance of Firmicutes (adj P < 0.01) observed in the BP35. The Firmicutes:Bacteroidetes ratio was significantly reduced in the BP95 diet (P < 0.01). The relative proportions of Proteobacteria (adj P < 0.01), Succinivibrionaceae (adj P < 0.03) and Succinivibrio (adj P = 0.053) increased in the BP95 diet. The abundance of Proteobacteria was found to be negatively associated with daily methane production (rs, −0.71; P < 0.01) and MPOMD (rs, −0.65; P < 0.01). Within Proteobacteria, the relationship of methane production was maintained with the mean abundance of Succinivibrio (rs, −0.69; P < 0.01). The abundance of the Firmicutes phyla was found to be positively correlated with both daily methane production (rs, 0.79; P < 0.001) and MPOMD (rs, 0.75; P < 0.01). Based on in vitro rumen simulation data, supplementation of an exclusively BP formulated concentrate was shown to reduce daily methane output by promoting a favorable alteration to the rumen prokaryotic community.

Effects of sulfonylurea herbicides chlorsulfuron and sulfosulfuron on enzymatic activities and microbial communities in two agricultural soils.

Sulfonylurea herbicides are widely used for weed control in agriculture, and they are suspected to alter microbial communities and activities in the soil. This study investigates the impact of two sulfonylurea herbicides chlorsulfuron and sulfosulfuron on microbial community and activity in two different soils taken from two sites in west part of the Slovak Republic. The soil from the Malanta site was silt-loam luvisol with pH(H2O) 5.78 while the soil from the Stefanov site was sandy-loam regosol with pH(H2O) 8.25. These soils were not treated by sulfonylurea herbicides at least for 2years prior to the study. In laboratory assay, the herbicides were applied to soil in their maximal recommended doses 26 and 25g per hectare of chlorsulfuron and sulfosulfuron, respectively. Their effect was evaluated on the 3rd, 7th, 14th, 28th, 56th, and 112th day after application to soil. Illumina high-throughput amplicon sequencing of the 16S rRNA gene and ITS region was used to monitor changes on prokaryotic and fungal community composition. Enzymatic activity was evaluated using 11 substrates. Physiological profile of microbial community was analyzed using Biolog© ecoplates. Significant changes in enzymatic activity caused by the application of herbicides were found during the first 28days. The application of herbicides altered the activity of cellobiohydrolase, arylsulphatase, dehydrogenase, phosphatase, and FDA hydrolase. Chlorsulfuron caused a more varying response of enzymatic activity than sulfosulfuron, and observed changes were not the same for both soils. In Malanta soil, chlorsulfuron decreased dehydrogenase activity while it was increased in the Stefanov soil. Phosphatase activity was decreased in both soils on 7th and 14th day. There were only minor changes in prokaryotic or fungal community or physiological profiles regarding pesticide application. Differences between soils and incubation time explained most of the variability in these parameters. Diversity indices, physiological parameters, and enzymatic activity decreased over time. The results have shown that chlorsulfuron and sulfosulfuron can affect the function and activity of the soil microbial community without significant change in its composition.

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil.

Composted sewage sludge (CSS) gained attention as a potential fertilizer in agriculture. Application of CSS increases soil microbial activity and microbial biomass, however, it can also lead to increased chemical and microbiological risks. In this study, we performed microcosm experiments to assess how CSS reshapes the microbial community of diluvial sand (DS) soil. Further, we assessed the potential of CSS to increase the persistence of human pathogens in DS soil and the colonization of Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt). The results revealed that CSS substantially altered the prokaryotic community composition. Moreover, addition of CSS increased the persistence of Salmonella enterica serovar Typhimurium strain 14028s and S. enterica serovar Senftenberg in DS soil. However, the enhanced persistence in soil had no impact on the colonization rate of B. rapa grown on soil inoculated with Salmonella. We detected Salmonella in leaves of 1.9% to 3.6% of plants. Addition of CSS had no impact on the plant colonization rate. The use of sewage sludge composts is an interesting option. However, safety measures should be applied in order to avoid contamination of crop plants by human pathogens.

Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea.

In natural environments, the production of neurotoxic and bioaccumulative methylmercury (MeHg) is mediated by microorganisms carrying the genes hgcA and hgcB. However, the contribution of these microorganisms to mercury (Hg) methylation or MeHg accumulation in the ocean is poorly understood. Here we determined the total Hg (THg) and MeHg concentrations in seawater samples and conducted a metagenomic survey of the hgcAB genes and functional modules involved in metabolic pathways in the East China Sea (ECS). In the metagenomic analyses, we used paired-end reads and assembled contigs for hgcAB enumeration and phylogenetic analyses in the seawater column. To evaluate the relative abundance of hgcAB in the metagenomic data, we estimated the abundance of recA (single-copy gene of bacteria) as well and then compared them. Moreover, the profiles of prokaryotic community composition were analyzed by 16S rRNA gene (V4 region) deep-sequencing. In the mesopelagic layers, the hgcA sequences were detected, and there was a positive correlation between hgcA abundance relative to the recA and MeHg concentrations. Thus, the quantification of the hgcA sequences could provide valuable information to evaluate the potential environments of microbial MeHg accumulation in the seawater column. A phylogenetic analysis using the assembled contigs revealed that all of the hgcA sequences in the mesopelagic layers were affiliated with Nitrospina-like sequences. The 16S rRNA gene analysis revealed that Nitrospinae were abundant in the mesopelagic layers. Although the lineages of Deltaproteobacteria, Firmicutes, and Spirochaetes were detected in the seawater column, their hgcAB sequences were not detected in our metagenomes, despite the fact that they are closely related to previously identified Hg methylators. The metabolic pathway analysis revealed that the modules related to sulfur and methane metabolism were prominent in the mesopelagic layers. However, no hgcA sequences affiliated with sulfate-reducing bacteria (SRB) or methanogens were detected in these layers, suggesting that these bacteria could not be strongly involved in the Hg accumulation in the seawater column. Our results indicate that Nitrospina-like bacteria with hgcAB genes could play a critical role in microbial Hg accumulation in the oxygenated mesopelagic layers of the ECS.

Temporal Changes in Microbial Communities Beneath Fish Farm Sediments Are Related to Organic Enrichment and Fish Biomass Over a Production Cycle

The marine fish farming industry is growing at a significant rate, yet a number of concerns still remain with regards to environmental impacts on the surrounding coastal sea and its biota. Here, we assessed the impact of intensive farming on benthic prokaryotic communities at a Mediterranean sea bass and sea bream intensive aquaculture site over a period of 10 months, in relation to the increase in fish biomass within the cage together with the organic matter enrichment in the sediments. We report positive relationships between prokaryotic abundance and both organic matter and fish biomass, and a contextual decrease in prokaryotic diversity below the cages. A significant shift in microbial community composition occurred in fish farm sediments (FF) over time, indicating a likely impact of ongoing aquaculture activity on prokaryotic communities. Among the dominant taxa at the impacted site, we found Epsilonproteobacteria and Bacteroidetes, which showed a general increase with fish biomass. Analyses on specialist taxa underlined significant contributions of Clostridiales and Bacteroidales in the farmed sediments. Finally, sea bream and sea bass gut microbiome-related taxa were detected during the sampling period. Our results indicate that prokaryotic community composition underneath the cages is related to fish biomass and organic enrichment over the course of production, and confirms that the study of benthic microbial communities at aquaculture sites represents a useful tool to assess the impact of intensive mariculture on the surrounding environment.

Prokaryotic Community Composition and Extracellular Polymeric Substances Affect Soil Microaggregation in Carbonate Containing Semiarid Grasslands

In the barren semiarid landscape individual plant species improve soil structure, reducing the erosion risks, whereby microaggregates form the most fundamental soil structural components. Extracellular polymeric substances (EPS) are considered as an important glue determining aggregation in addition to inorganic binding agents such as carbonates. However, the role of the prokaryotic community in EPS formation and consequently for microaggregation in natural environments is not substantially clarified yet. EPS should be particularly important under semiarid conditions as it forms a protection mechanisms of the prokaryotes against desiccation. Therefore, we examined the influence of the prokaryotic community on soil EPS content and subsequently on soil microaggregation in semiarid grasslands, depending on the parent material, common plant species and the distance to the plant. Soil samples were taken over a distance gradient from two major semiarid grassland plant species in Southern Spain, the legume shrub Anthyllis cytisoides and the grass tussock Macrochloa tenacissima, to the surrounding bare soil at two sites, rich and poor in carbonates. Total community DNA and EPS were extracted, followed by quantification of EPS-saccharide and bacterial abundance and examination of the prokaryotic community composition. Further, the particle size distribution of the microaggregate fraction was determined as an indication of microaggregation. We found that the overall prokaryotic community composition differed between the two sites, but not between plant species. Nonetheless, a link between the community composition and EPS content was established, whereby soil organic matter (OM) seems to be a regulating factor as increasing soil OM contents resulted in more EPS-saccharide. Furthermore, microaggregation was enhanced by the canopy, especially at the edge of Macrochloa tussocks. Contrary to the expectation that increasing inorganic C contents would diminish importance of EPS, the parent material richest in inorganic C results in a significant effect of EPS-saccharide content on microaggregation. For the inorganic C poor site, EPS-saccharide had no observed direct effect on microaggregation. Based on our results we conclude that the availability of decomposable OM influences the prokaryotic community composition and thereby triggers EPS production whereas large contents of polyvalent cations promote the stabilizing effect of EPS on microaggregates.

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location.

Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown. In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous) and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and evenness of prokaryotic and eukaryotic microbial communities in lakes across elevation and N deposition gradients in the Sierra Nevada mountains of California, USA. We found that both prokaryotic and eukaryotic communities are structured by temperature, terrestrial (allochthonous) DOC and latitude. Prokaryotic communities are also influenced by total and aquatic (autochthonous) DOC, while eukaryotic communities are also structured by nitrate. Additionally, increasing N availability was associated with reduced richness of prokaryotic communities, and both lower richness and evenness of eukaryotes. We did not detect any synergistic or antagonistic effects as there were no interactions among temperature and resource variables. Together, our results suggest that (a) organic and inorganic resources, temperature, and geographic location (based on latitude and longitude) independently influence lake microbial communities; and (b) increasing N supply due to atmospheric N deposition may reduce richness of both prokaryotic and eukaryotic microbes, probably by reducing niche dimensionality. Our study provides insight into abiotic processes structuring microbial communities across environmental gradients and their potential roles in material and energy fluxes within and between ecosystems.

Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system

Abstract. We experimentally evaluated the temporal (interday and interseason) and spatial variability in microbial plankton responses to vitamin B12 and/or B1 supply (solely or in combination with inorganic nutrients) in coastal and oceanic waters of the northeast Atlantic Ocean. Phytoplankton and, to a lesser extent, prokaryotes were strongly limited by inorganic nutrients. Interday variability in microbial plankton responses to B vitamins was limited compared to interseason variability, suggesting that B-vitamin availability might be partially controlled by factors operating at seasonal scale. Chlorophyll a (Chl a) concentration and prokaryote biomass (PB) significantly increased after B-vitamin amendments in 13 % and 21 %, respectively, of the 216 cases (36 experiments × 6 treatments). Most of these positive responses were produced by treatments containing either B12 solely or B12 combined with B1 in oceanic waters, which was consistent with the significantly lower average vitamin-B12 ambient concentrations compared to that in the coastal station. Negative responses, implying a decrease in Chl a or PB, represented 21 % for phytoplankton and 26 % for prokaryotes. Growth stimulation by B1 addition was more frequent on prokaryotes than in phytoplankton, suggesting that B1 auxotrophy in the sampling area could be more widespread in prokaryotes than in phytoplankton. Negative responses to B vitamins were generalized in coastal surface waters in summer and were associated with a high contribution of Flavobacteriales to the prokaryote community. This observation suggests that the external supply of B12 and/or B1 may promote negative interactions between microbial components when B-vitamin auxotrophs are abundant. The microbial response patterns to B12 and/or B1 amendments were significantly correlated with changes in the prokaryotic community composition, highlighting the pivotal role of prokaryotes in B-vitamin cycling in marine 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.

Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems

The rhizosphere microbiome plays an important role in disease-suppressive soils and is closely related to plant health. While a key role of plant-related factors in shaping the rhizosphere microbiome is well known for natural ecosystems and similarly fertilized agricultural systems, the interaction between fertilization and plant species effects on rhizosphere microbial communities has less been determined. Here, we assessed the influence of plant- and fertilization-related factors on the abundance, biomass and composition of rhizosphere and bulk soil prokaryotic communities. Soil samples were collected from the bulk soil and the rhizosphere of maize, potato, and white mustard under mineral (N180P150K150 per year) and organic (50 t ha−1 of fresh cattle manure) fertilization treatments within a long-term microplot experiment. Total (DNA) and potentially active (RNA) prokaryotic communities were analyzed using RT-PCR and Illumina MiSeq amplicon sequencing. Both NPK and manure fertilization systems led to the similarity of the prokaryotic community structures in rhizosphere and bulk soil. Long-term application of manure increased significantly prokaryotic abundance and diversity due to development of many underrepresented taxa. NPK significantly reduced prokaryotic diversity and the total number of species. Our findings suggest that fertilization is a more important factor in determining the abundance and diversity of prokaryotic communities in the rhizosphere than plant species. Thus, the traditional concept of the key role of plant species in shaping prokaryotic communities in the rhizosphere which is valid for non-cultivated plant species was not confirmed for the agricultural ecosystems and crops investigated here.

Impact of the application of commercial and farm-made fermented liquid organic amendments on corn yield and soil quality

Organic amendments are being increasingly applied to agricultural soils as alternatives or complements to inorganic fertilizers. Organic amendments can increase the content of soil organic matter, concomitantly improving soil physical, chemical and biological properties. We evaluated the effect of the application of commercial vs. farm-made fermented liquid organic amendments, compared to mineral (NPK) fertilization, on corn yield and nutritional status, as well as on soil physicochemical and microbial properties as indicators of soil quality. In particular, we assessed the effect of two doses (optimal vs. suboptimal) and times of amendment application (basal dressing vs. basal + top dressing) for two consecutive growing seasons. Values of corn grain yield were lower in organically-amended plots than in those under NPK fertilization. At the optimal dose, the application of organic amendments led to significantly higher values of microbial activity (soil respiration; enzyme activities; potentially mineralizable N) and biomass (microbial biomass C, bacterial and fungal biomass), leading to an improvement in soil quality. The optimal application dose resulted in an enhanced soil nutrient pool. Conversely, soil properties were not significantly affected by the origin of the amendment (commercial vs. farm-made) or the time of application (basal dressing vs. basal + top dressing). 16S rRNA metabarcoding analysis revealed no significant changes in the diversity and composition of the soil prokaryotic communities between organically-amended and NPK-fertilized soils. It was concluded that the application of fermented liquid organic amendments at the optimal dose (according to the N requirements of corn) can be a beneficial agronomic practice for agricultural soil quality, posing a suitable alternative to mineral fertilization.