Changes In Bacterial Community Composition Research Articles

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.

Responses of Intertidal Bacterial Biofilm Communities to Increasing pCO2.

The effects of ocean acidification on ecosystems remain poorly understood, because it is difficult to simulate the effects of elevated CO2 on entire marine communities. Natural systems enriched in CO2 are being used to help understand the long-term effects of ocean acidification in situ. Here, we compared biofilm bacterial communities on intertidal cobbles/boulders and bedrock along a seawater CO2 gradient off Japan. Samples sequenced for 16S rRNA showed differences in bacterial communities with different pCO2 and between habitat types. In both habitats, bacterial diversity increased in the acidified conditions. Differences in pCO2 were associated with differences in the relative abundance of the dominant phyla. However, despite the differences in community composition, there was no indication that these changes would be significant for nutrient cycling and ecosystem function. As well as direct effects of seawater chemistry on the biofilm, increased microalgal growth and decreased grazing may contribute to the shift in bacterial composition at high CO2, as documented by other studies. Thus, the effects of changes in bacterial community composition due to globally increasing pCO2 levels require further investigation to assess the implications for marine ecosystem function. However, the apparent lack of functional shifts in biofilms along the pCO2 gradient is a reassuring indicator of stability of their ecosystem functions in shallow ocean margins.

Effects of Composting Different Types of Organic Fertilizer on the Microbial Community Structure and Antibiotic Resistance Genes.

Organic fertilizer is a major carrier that stores and transmits antibiotic resistance genes (ARGs). In the environment, due to the application of organic fertilizers in agriculture, the increasing diversity and abundance of ARGs poses a potential threat to human health and environmental safety. In this paper, the microbial community structure and ARGs in different types of organic fertilizer treated with composting were examined. We found that the abundance and diversity of ARGs in earthworm cast organic fertilizer were the lowest and the highest in chicken manure organic fertilizer. Interestingly, the abundance and diversity of ARGs, especially beta-lactam resistance genes, sulfonamide resistance genes, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes, in organic fertilizers were reduced significantly, while composting caused no significant change in mobile genetic elements (MGEs), where antibiotic deactivation and the use of efflux pumps were the two most dominant mechanisms. It was clear that removal of ARGs became more efficient with increasing reduction in the bacterial abundances and diversity of potential ARG hosts, and integron-mediated horizontal gene transfers (HGTs) played an important role in the proliferation of most ARG types. Therefore, the reduction in ARGs was mainly driven by changes in bacterial community composition caused by composting. Furthermore, rather than HGTs, the diversity and abundance of bacterial communities affected by compost physical and chemical properties were the main drivers shaping and altering the abundance and diversity of ARGs, which was indicated by a correlation analysis of these properties, antibiotic residues, microbial community structure, and ARGs. In general, high-temperature composting effectively removed antibiotic residues and ARGs from these organic fertilizers; however, it cannot prevent the proliferation of MGEs. The insights gained from these results may be of assistance in the safe and rational use of organic fertilizers by indicating the changes in microbial community structure and ARGs in different types of organic fertilizer treated with composting.

Vertical changes in bacterial community composition down to a depth of 20 m on the degraded Loess Plateau in China

AbstractSoil microbes are involved in the fundamental processes that underpin an ecosystem's function. However, little is known about the microbial communities that inhabit deep soil horizons, especially in degraded forest ecosystems. Here, we used high‐throughput sequencing to investigate the vertical distribution of soil bacterial communities to a depth of 20 m in Pinus tabulaeformis and Robinia pseudoacacia forests on the Loess Plateau, China. We found that bacterial richness declined from the topsoil to a depth of 2 m in P. tabulaeformis forests and declined from the topsoil to a depth of 1 m in R. pseudoacacia forests, and thereafter increased. The relative abundance of α‐Proteobacteria was higher in subsoils than in topsoils of P. tabulaeformis forests. It was highest at the depth of 20 or 14 m in both forest types, suggesting that α‐Proteobacteria can survive dry, alkaline, low‐nutrient environments. We also found a higher relative abundance of Acidobacteria in topsoils than in subsoils, indicating that Acidobacteria can grow well in nutrient‐rich environments. Our results suggest that soil bacterial communities respond to nutrient changes associated with soil depth and plant species. These findings revealed that soil microorganisms persisted in deep and carbon‐starved soils, especially for α‐Proteobacteria, which may be adapted to resource‐poor environments in deep soils.

Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum

Abstract. The Rajang River is the main drainage system for central Sarawak in Malaysian Borneo and passes through peat domes through which peat-rich material is being fed into the system and eventually into the southern South China Sea. Microbial communities found within peat-rich systems are important biogeochemical cyclers in terms of methane and carbon dioxide sequestration. To address the critical lack of knowledge about microbial communities in tropical (peat-draining) rivers, this study represents the first seasonal assessment targeted at establishing a foundational understanding of the microbial communities of the Rajang River–South China Sea continuum. This was carried out utilising 16S rRNA gene amplicon sequencing via Illumina MiSeq in size-fractionated samples (0.2 and 3.0 µm GF/C filter membranes) covering different biogeographical features and sources from headwaters to coastal waters. The microbial communities found along the Rajang River exhibited taxa common to rivers (i.e. predominance of β-Proteobacteria) while estuarine and marine regions exhibited taxa that were common to the aforementioned regions as well (i.e. predominance of α− and γ-Proteobacteria). This is in agreement with studies from other rivers which observed similar changes along salinity gradients. In terms of particulate versus free-living bacteria, nonmetric multi-dimensional scaling (NMDS) results showed similarly distributed microbial communities with varying separation between seasons. Distinct patterns were observed based on linear models as a result of the changes in salinity along with variation of other biogeochemical parameters. Alpha diversity indices indicated that microbial communities were higher in diversity upstream compared to the marine and estuarine regions, whereas anthropogenic perturbations led to increased richness but less diversity. Despite the observed changes in bacterial community composition and diversity that occur along the continuum of the Rajang River to the sea, the PICRUSt predictions showed minor variations. The results provide essential context for future studies such as further analyses on the ecosystem response to anthropogenic land-use practices and probable development of biomarkers to improve the monitoring of water quality in this region.

Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition

Soil fumigation is currently the most effective method for controlling soil-borne pests and diseases in high-value crops. To better understand the effect of chloropicrin (CP), dazomet (DZ), dimethyl disulfide (DMDS), allyl isothiocyanate (AITC) and 1,3-dichloropropene (1,3-D) fumigants on soil microorganisms, this study monitored changes in the diversity and community composition of soil bacteria involved in denitrification using real-time PCR and high-throughput gene sequencing techniques. These five fumigants significantly decreased the bacterial population size in some phyla including Proteobacteria, Chloroflexi and Acidobacteria, and increased the bacterial population size in other phyla such as Firmicutes, Gemmatimonadetes, Actinobacteria, Verrucomicrobia, Saccharibacteria and Parcubacteria. Although bacterial diversity declined after CP fumigation, it was briefly stimulated by the other four fumigants. Meanwhile, all five fumigants temporarily decreased populations of denitrifying bacteria containing the napA, narG, nirS or nirK enzyme-encoding genes. Denitrifiers bearing the cnorB, qnorB or nosZ genes were relatively stable following DZ and DMDS fumigation. However, cnorB and nosZ decreased initially following CP, AITC and 1,3-D fumigation. Simultaneously, the abundance of qnorB significantly increased in AITC and 1,3-D fumigated soils. These results showed that soil fumigation significantly shifted the abundance and community structure of denitrifying bacteria. This study will help to predict the response of different phyla of denitrifying bacteria to soil fumigation.

Respiratory Dysbiosis in Canine Bacterial Pneumonia: Standard Culture vs. Microbiome Sequencing.

It is unknown how the respiratory microbiome influences and is influenced by bacterial pneumonia in dogs, as culture of lung samples and not microbial sequencing guides clinical practice. While accurate identification of pathogens are essential for treatment, not all bacteria are cultivable and the impact of respiratory dysbiosis on development of pneumonia is unclear. The study purposes were to (1) characterize the lung microbiome in canine bacterial pneumonia and compare deviations in dominant microbial populations with historical healthy controls, (2) compare bacteria identified by culture vs. 16S rDNA sequencing from bronchoalveolar lavage fluid (BALF) culture-, and (3) evaluate similarities in lung and oropharyngeal (OP) microbial communities in community-acquired and secondary bacterial pneumonia. Twenty BALF samples from 15 client-owned dogs diagnosed with bacterial pneumonia were enrolled. From a subset of dogs, OP swabs were collected. Extracted DNA underwent PCR of the 16S rRNA gene. Relative abundance of operational taxonomic units (OTUs) were determined. The relative abundance of bacterial community members found in health was decreased in dogs with pneumonia. Taxa identified via culture were not always the dominant phylotype identified with sequencing. Dogs with community-acquired pneumonia were more likely to have overgrowth of a single organism suggesting loss of dominant species associated with health. Dogs with secondary bacterial pneumonia had a greater regional continuity between the upper and lower airways. Collectively, these data suggest that dysbiosis occurs in canine bacterial pneumonia, and culture-independent techniques may provide greater depth of understanding of the changes in bacterial community composition that occur in disease.

Soil chloride content influences the response of bacterial but not fungal diversity to silver nanoparticles entering soil via wastewater treatment processing

Silver nanoparticles (NPs) are among the most widely used nanomaterials and are entering soil ecosystems, mainly via biosolids in agriculture. When added directly to soils, metallic Ag-NPs have been shown to affect microbial communities, which underpin important ecosystem functions. During wastewater treatment processing, metallic Ag-NPs are rapidly converted to Ag2S, which is relatively insoluble and less toxic. Furthermore, recent evidence indicates that silver bioavailability is influenced by soil chloride content. Hence there is a need to understand how Ag2S, which forms from Ag-NPs during wastewater treatment, influences soil microbial diversity at varying salinity. In this study, after adding Ag-NPs to sludge (with most converted to Ag2S), we then applied the sludge to soil and examined how salinity influences the effects of 0 mg, 1 mg and 10 mg kg−1 Ag on bacterial and fungal diversity over time. Using high-throughput phylogenetic marker gene sequencing of 16S rRNA gene and ITS2 amplicons, we demonstrate that, despite being theoretically less toxic, wastewater treatment processed Ag-NPs can affect the composition of soil bacterial and fungal communities, and influence bacterial alpha diversity. In addition, we found that silver-associated changes in bacterial community composition were affected by soil chloride content, with more acute responses to silver being observed in more saline soils. This work highlights that the release of Ag-NPs and their conversion into Ag2S prior to addition to soils via realistic exposure pathways can alter microbial diversity and that these effects may be influenced by soil chloride content.

Spatial and temporal succession of bacterial communities in three artificial fishponds

Fishponds are artificial yet dynamic environments. Microbes play a vital role in the conversion and metabolism of organic matter in aquaculture environments such as fishponds. Changes in bacterial community composition in three fishponds over a 5-month period were investigated by sequencing the 16S rRNA gene through Illumina Miseq. A total of 2,195,879 sequences and 9,975 operational taxonomic units (OTUs) were obtained. Further analysis showed that the dominant phyla in three ponds were similar, including Proteobacteria, and Bacteroidetes. A comprehensive analysis of the diversity, redundancy analysis (RDA) and partial redundancy analysis (pRDA) showed a spatial-temporal structural pattern in the bacterial communities. The bacterial community composition in the three fishponds was shaped more by spatial variation than by temporal variation. The effect of pond isolation was emphasized by the significant differences observed in the three fishponds. However, the temporal succession of bacterial communities in each pond exhibited a similar trend. Correlation analysis and RDA also indicated that temporal variation was significantly associated with TOC, TN and NO2−. This study would improve our understanding of the assembly mechanisms of a microbial structure in artificial pond ecosystems, and provide useful information for fishpond management.

Contribution of soil variables to bacterial community composition following land use change in Napahai plateau wetlands

Land use changes have significant modifications on soil conditions, which is likely to induce alterations in the soil bacterial communities. Little is known about the respective contributions of soil variables to these changes in bacterial communities. For this study, high-throughput sequencing technology was applied to measure the change in bacterial community compositions under the effects of soil variables across three land-use types (i.e., reference, degraded, and agricultural wetlands) in the Napahai plateau. Compared with the reference wetland, a pronounced decrease (1.5–5.3 times) in soil water content, soil organic matter, and total and available nitrogen was observed in degraded and agricultural wetlands. However, a conspicuous increase (1.3–5.7 times) was found for the total and available phosphorus, and potassium. Land use also strongly affected the taxonomic composition of soil bacterial assemblages, changing the normalized ratio of Acidobacteria to Proteobacteia, or to δ-proteobacteia. Soil properties had different contributions to the variations in abundance composition of bacterial community. Soil available phosphorus and potassium were the best predictors for changes in bacterial community composition, explaining 80.9% and 82% of the variations, respectively. In contrast, soil organic matter, carbon/nitrogen, total phosphorus, and total and available nitrogen accounted for 58.7–72.7% of the variations in bacterial community composition. Soil pH (24.6%) and soil water content (40.4%) had a minor contribution. Our data suggested that the compositional alterations of microbial communities following land-use change were likely realized through modifications in the availability of primary soil nutrients in the Napahai plateau wetlands.

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study.

The aerial surfaces of plants harbor diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterized the epiphytic microbial communities on leaves of Platanus × hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree’s phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city center compared to the natural site, and also more human-associated genera were found colonizing the leaves from the city center. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.

Dynamic changes in fermentation profiles and bacterial community composition during sugarcane top silage fermentation: A preliminary study

Investigating the dynamic changes in bacterial community composition during sugarcane top silage production starting in late March and finishing in late June (storage temperature: 20 to 35 °C) will advance our understanding of ensilage in hot ambient temperatures. The results showed that, the fermentation process was dominated by Leuconostocaceae (until d 5), followed by Lactobacillaceae (from d 5 to d 30), and finally Lactobacillaceae and Clostridium (from d 60 to d 90). As the fermentation process progressed, there was a significant increase in Lactobacillaceae abundance, and on d 60 there was a sharp increase in Clostridiaceae abundance. Spearman’s correlation showed that, Lactococcus and Leuconostoc abundance were negatively correlated with acetate, propionate, butyrate, and ammonia-N levels. Clostridiaceae and Lactobacillaceae abundance were positively correlated with acetate, propionate, butyrate, and ammonia-N levels. The high moisture content (DM 24.31%) of sugarcane tops stored in hot ambient temperatures may result in butyric acid fermentation.

Biochar as a management tool for soilborne diseases affecting early stage nursery seedling production

Biochar is thought to have great potential as a supplemental amendment in nursery growing media. The knowledge of how to optimize the use of biochar in the nursery setting during the most vulnerable pre-emergence and early seedling stages of the plant, however, is underdeveloped. The current study involves pre-emergence trials in the Pythium aphanidermatum-cucumber pathosystem using a commercial nursery potting mixture amended with up to 3% w:w wood-derived biochar. The major questions were: (i) is pre-conditioning required to elicit suppression of pre-emergence damping-off disease in the Pythium-cucumber system; (ii) what are the changes in bacterial community composition and diversity due to pre-conditioning of the biochar-amended potting medium; and (iii) can the pre-conditioning stage be shortened from 45 days and still provide disease suppression. Pre-conditioning, consisting of pre-planting fertigation of the nursery medium, was found to be needed to achieve suppression of damping-off disease by biochar, with a reduction in pre-emergence damping-off caused by P. aphanidermatum by up to 71%. Illumina sequencing of 16s bacterial gene revealed a significant enrichment in the abundance of bacteria in general and potentially beneficial microorganisms in particular, as well as shifts in microbial community structure as a result of biochar addition. These changes may play an important role in the overall effects of biochar on disease suppression in young seedlings. A pre-conditioning period of only 14 days was found to be effective for disease suppression, which can substantially improve its practical utility for nurseries.

Changes in bacterial community composition across natural grassland and pine forests in the Bunya Mountains in subtropical Australia

Tree and grass species coexist in many ecosystems worldwide and support multiple ecosystem functions and services. However, the distribution of bacterial communities and factors driving coexistence in tree–grass associations and their ecosystem functions remain poorly understood. In this study, the distribution of soil bacteria and their link to changes in abiotic factors were investigated in adjacent montane grassland (C4 plants) and pine forest (bunya pine and hoop pine; C3 plants) sites in the Bunya Mountains, subtropical Australia. Different vegetation (grassy balds and forest) had a substantial effect on terrestrial ecosystem properties, with higher levels of soil nutrients (e.g. total nitrogen (N), total phosphorus (P)) and electrical conductivity (EC), and lower δ13C values and pH under forests compared with grassland. Bacterial α-diversity (total species per operational taxonomic unit richness) did not differ between grassland and pine forest sites, whereas strong shifts in the bacterial community composition and structure were evident. Patterns in bacterial community structure were strongly associated with changes in soil pH, EC, total P and δ13C. Different bacterial groups associated with pine forest (Gammaproteobacteria and Alphaproteobacteria) and grassland (Acidobacteria and Verrucomicrobia) were identified as key groups contributing to the segregation of these two ecosystems in the Bunya Mountains. These findings suggest that heterogeneity in soil edaphic properties (e.g. key nutrients) likely contributed to variation in bacterial β-diversity of grassland and pine forest, which has potential implications for species coexistence and ecosystem function in montane eastern Australia.

A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa.

SummaryIn many studies, rare bacterial taxa have been found to increase in response to environmental changes. These changes have been proposed to contribute to the insurance of ecosystem functions. However, it has not been systematically tested if rare taxa are more likely to increase in abundance than dominant taxa. Here, we study whether rare soil bacterial taxa are more likely to respond to environmental disturbances and if rare taxa are more opportunistic than dominant taxa. To test this, we applied nine different disturbance treatments to a grassland soil and observed changes in bacterial community composition over 7 days. While 12% of the dominant taxa changed in abundance, only 1% of the rare taxa showed any effect. Rare taxa increased in response to a single disturbance treatment only, while dominant taxa responded to up to five treatments. We conclude that rare taxa are not more likely to contribute to community dynamics after disturbances than dominant taxa. Nevertheless, as rare taxa outnumber abundant taxa with here 230 taxa that changed significantly, the chance is high that some of these rare taxa might act as ecologically important keystone taxa. Therefore, rare and abundant taxa might both contribute to ecosystem insurance.

Transition of Ethiopian highland forests to agriculture-dominated landscapes shifts the soil microbial community composition

BackgroundLand use changes and related land management practices significantly alter soil physicochemical properties; however, their effects on the soil microbial community structure are still unclear. In this study, we used automated ribosomal intergenic spacer analysis to determine the fungal and bacterial community composition in soils from different land use areas in the Ethiopian highlands. Soil samples were collected from five areas with different land uses, natural forest, eucalyptus plantation, exclosure, grassland and cropland, which had all historically been natural forest.ResultsOur results showed a significant shift in the soil bacterial and fungal community composition in response to land use change. We also identified soil physicochemical factors corresponding to the changes in bacterial and fungal communities. Although most soil attributes, including soil organic carbon, total soil nitrogen, labile P, soil pH and soil aggregate stability, were related to the change in bacterial community composition, the total soil nitrogen and soil organic carbon had the strongest relationships. The change in fungal community composition was correlated with soil nutrients, organic carbon, soil nitrogen and particularly the labile P concentration.ConclusionsThe fungal community composition was likely affected by the alteration of vegetation cover in response to land use change, whereas the bacterial communities were mainly sensitive to changes in soil attributes. The study highlights the higher sensitivity of fungal communities than bacterial communities to land use changes.

Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions.

There is a growing interest of overcoming the uncertainty related to the cumulative impacts of multiple disturbances of different nature in all ecosystems. With global change leading to acute environmental disturbances, recent studies demonstrated a significant increase in the possible number of interactions between disturbances that can generate complex, non-additive effects on ecosystems functioning. However, how the chronology of disturbances can affect ecosystems functioning is unknown even though there is increasing evidence that community assembly history dictates ecosystems functioning. Here, we experimentally examined the importance of the disturbances chronology in modulating the resilience of soil microbial communities and N-cycle related functions. We studied the impact of 3-way combinations of global change related disturbances on total bacterial diversity and composition, on the abundance of N-cycle related guilds and on N-cycle related activities in soil microcosms. The model pulse disturbances, i.e., short-term ceasing disturbances studied were heat, freeze-thaw and anaerobic cycles. We determined that repeated disturbances of the same nature can either lead to the resilience or to shifts in N-cycle related functions concomitant with diversity loss. When considering disturbances of different nature, we demonstrated that the chronology of compounded disturbances impacting an ecosystem determines the aggregated impact on ecosystem properties and functions. Thus, after 3 weeks the impact of the ‘anoxia/heat/freeze-thaw’ sequence was almost two times stronger than that of the ‘heat/anoxia/freeze-thaw’ sequence. Finally, we showed that about 29% of the observed variance in ecosystem aggregated impact caused by series of disturbances could be attributed to changes in the microbial community composition measured by weighted UniFrac distances. This indicates that surveying changes in bacterial community composition can help predict the strength of the impact of compounded disturbances on N-related functions and properties.

Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.

Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.

Impact of a Major Inflow Event on the Composition and Distribution of Bacterioplankton Communities in the Baltic Sea

Major Baltic inflow (MBI) events carry highly saline water from the North Sea to the central Baltic Sea and thereby affect both its environmental conditions and its biota. While bacterioplankton communities in the Baltic Sea are strongly structured by salinity, how MBIs impact the composition and distribution of bacteria is unknown. The exceptional MBI in 2014, which brought saline and oxygenated water into the basins of the central Baltic Sea, enabled the linkage of microbiological investigations to hydrographic and modelling studies of this MBI. Using sequence data of 16S ribosomal RNA (rRNA) and 16S rRNA genes (rDNA), we analyzed bacterioplankton community composition in the inflowing water and in the uplifted former bottom water at stations reached by the MBI. Bacterial diversity data were compared with respective data obtained from previous, non-inflow conditions. Changes in bacterial community composition following the 2014 MBI were mainly apparent at the genus level. A number of specific taxa were enriched in the inflowing water, with large changes in the rRNA/rDNA ratios indicating the different activity levels between of the water masses. The relative similarity of the bacterial communities in the inflowing and uplifted waters as well as the results from an inflow-simulating numerical model showed that the inflowing water did not originate directly from the North Sea but mostly from adjacent areas in the Baltic Sea. This suggested that the inflow event led to a series of shifts in Baltic Sea water masses among the Baltic Sea basins and a gradual mixing of the water bodies. Dramatic changes in the bacterial community composition occurred when the bottom-water inflow reached the anoxic, sulfidic deep basins, resulting in an uplifting of the formerly anoxic bacterial community, dominated by Epsilonproteobacteria. Our study of the impact of MBIs on bacterioplankton communities therefore highlights two relevant underlying mechanisms that impact the distribution and possibly also the activities of planktonic bacteria in the Baltic Sea: (1) the successive dilution of inflowing North Sea water with ambient waters and (2) the uplifting of former bottom-water communities to higher water strata.

Responses of Nitrogen-Cycling Microorganisms to Dazomet Fumigation.

The influence of soil fumigation on microorganisms involved in transforming nitrogen remains little understood, despite the use of fumigants for many decades to control soil-borne pathogens and plant-parasitic nematodes. We used real-time PCR (quantitative polymerase chain reaction) and 16S rRNA gene amplicon sequencing techniques to monitor changes in the diversity and community structure of microorganisms associated with nitrogen transfer after the soil was fumigated with dazomet (DZ). We also examined nitrous oxide (N2O) emissions from these microorganisms present in fumigated fluvo-aquic soil and lateritic red soil. Fumigation with DZ significantly reduced the abundance of 16S rRNA and nitrogen cycling functional genes (nifH, AOA amoA, AOB amoA, nxrB, narG, napA, nirK, nirS, cnorB, qnorB, and nosZ). At the same time, N2O production rates increased between 9.9 and 30 times after fumigation. N2O emissions were significantly correlated with , dissolved amino acids and microbial biomass nitrogen, but uncorrelated with functional gene abundance. Diversity indices showed that DZ temporarily stimulated bacterial diversity as well as caused a significant change in bacterial community composition. For example, DZ significantly decreased populations of N2-fixing bacteria Mesorhizobium and Paenibacillus, nitrifiers Nitrosomonas, and the denitrifiers Bacillus, Pseudomonas, and Paracoccus. The soil microbial community had the ability to recover to similar population levels recorded in unfumigated soils when the inhibitory effects of DZ fumigation were no longer evident. The microbial recovery rate, however, depended on the physicochemical properties of the soil. These results provided useful information for environmental safety assessments of DZ in China, for improving our understanding of the N-cycling pathways in fumigated soils, and for determining the potential responses of different N-cycling groups after fumigation.