Environmental Stress Shapes Bacterial Community Structure and Function Through Interactive Abiotic Effects.

The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24-38% and 17-39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17-32% and 15-20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally 'redundant'. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water.

In order to clarify the effects of mixture intercropping on the control of rice blast and the structure and function of the rhizosphere bacterial community, the 16S rRNA sequencing analysis of bacteria in rhizosphere soil of the selected high control efficiency (E=54.48%) (Shanyou 63/Huangkenuo) and low control efficiency (E=14.12%) combinations (Hexi 39/Huangkenuo) under the intercropping and monoculture treatments were performed with Illumina Hiseq sequencing technology. The results showed that soil bacteria, from 37 phyla, 116 classes, 244 orders, 384 families, 689 genera, were obtained in the intercropping system. Chloroflexi, Proteobacteria, and Actinobacteriota were the dominant bacterial groups. The relative abundance was higher than 15%. Alpha diversity analysis discovered that high-efficacy combination significantly increased the Shannon index and Chao1 index of rice rhizosphere bacterial community in intercropping conditions (<italic>P</italic>&lt;0.05), whereas there was no difference at <italic>P</italic>&gt;0.05 in low-efficiency combination. ANOSIM and PCoA analyses revealed that there was significant difference in the structure of the species in the rhizosphere bacterial community in monoculture (<italic>r </italic>= 0.48, <italic>P</italic>&lt;0.01), but no significant difference in the rhizosphere bacterial community structure between the high- and low-efficiency combinations following intercropping (<italic>P</italic>&gt;0.05), which indicating that intercropping increased the similarity of bacterial community structure between both combinations. Comparison to monoculture, the dominant bacterial group composition proved that the relative abundance of Shanyou63 Acidobacteriota decreased significantly, while the relative abundance of Shanyou 63 Actinobacteriota and Firmicutes increased significantly, but there was no significant difference among the dominant bacteria in Huangkenuo. Hexi 39 rhizosphere Patescilbacteria exhibited the significant decrease in low-efficiency combinations, whereas Gemmatimonadota showed the significant increase. PICRUSt2 function prediction discovered that the relative abundance of biosynthesis of other secondary metabolites in the main cultivars decreased significantly in the intercropping system, while the relative abundance of transcription, metabolism of cofactors and vitamins in intercropping cultivars increased significantly. In conclusion, to increase plant disease resistance and to provide data support for the theory of diverse intercropping for disease control, the high-efficacy combination had the ability to improve the diversity of rice rhizosphere bacteria and the structure and function of bacterial community by mixture intercropping, which effectively reduced the occurrence of rice blast and provided an application pathway for the improvement of soil microorganisms.

Ultramafic soils are characterized by high levels of metals, and have been studied because of their geochemistry and its relation to their biological component. This study evaluated soil microbiological functioning (SMF), richness, diversity, and structure of bacterial communities from two ultramafic soils and from a non-ultramafic soil in the Brazilian Cerrado, a tropical savanna. SMF was represented according to simultaneous analysis of microbial biomass C (MBC) and activities of the enzymes β-glucosidase, acid phosphomonoesterase and arylsulfatase, linked to the C, P and S cycles. Bacterial community diversity and structure were studied by sequencing of 16S rRNA gene clone libraries. MBC and enzyme activities were not affected by high Ni contents. Changes in SMF were more related to the organic matter content of soils (SOM) than to their available Ni. Phylogeny-based methods detected qualitative and quantitative differences in pairwise comparisons of bacterial community structures of the three sites. However, no correlations between community structure differences and SOM or SMF were detected. We believe this work presents benchmark information on SMF, diversity, and structure of bacterial communities for a unique type of environment within the Cerrado biome.

Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa

Urbanization is an important ecological modifier of stream catchments and significantly alters C type and concentration and heavy metal input to aquatic systems. C and heavy metals are important determinants of microbial community structure (population dynamics) and function (physiological processes). Understanding how changes at the landscape scale affect key nutrient-transformation processes (e.g., denitrification) and C metabolism (e.g., methanogenesis) at the micro scale requires simultaneous determination of the structural and functional responses of bacterial communities. We compared total bacterial (16S ribosomal ribonucleic acid [rRNA] gene) and denitrifying bacterial (nosZ gene) community structures in sediments taken from an urban and a nonurban stream before and after C and Zn additions. Microcosms containing stream sediment were supplemented with either proteinaceous or leaf-leachate C, increasing the C content by ∼36 and 130 mg/L, respectively. C was added in the presence and absence ...

To reveal the effects of biogas slurry application on soil microbial community structure and function, a soil column experiment was constructed with three treatments[(no N addition, CM; conventional fertilization, SN; biogas slurry addition, SZ)]. The differences in composition, diversity, and structure of bacterial and fungal communities on day 1 and day 21 after soil flooding were evaluated, and their functions were predicted using Illumina high-throughput sequencing technology. The results of the analysis of α diversity showed that the fungal α-diversity indexes of CM, SN, and SZ treatments on day 1 were significantly higher than those on day 21, and there was no significant difference among the three treatments. However, the bacterial Simpson index differed among the three treatments on day 21, with SZ-21 showing a higher Simpson index but lower Chao1 index compared with those of SZ-21. The analysis of bacterial community structure showed that Firmicutes, Chloroflexi, and Actinobacteria in the SN-1 treatment were different from those in the other treatments on day 1, whereas the relative abundance of bacterial phyla in the SZ and SN treatments were similar on day 21. The analysis of fungal community structure showed that the relative abundance of Ascomycota and Zygomycota in the SZ-1 treatment were higher than those in the SN-1 and CM-1 treatments on day 1. The relative abundance of Ascomycota in the SN-21 and SZ-21 treatments were lower, whereas that of Zygomycota were higher compared with that in CM-21. The analysis of NMDS showed that the composition of bacterial and fungal communities in the SN and SZ treatments showed a gradually similar trend. The PICRUSt analysis showed that the function of the soil bacterial community was similar in the CM, SN, and SZ treatments. The FUNGuild function prediction reflected that the main differences in trophic type between the SN-21 and SZ-21 treatments occurred in saprotroph and pathotroph forms. Therefore, biogas slurry addition in the wheat-rice stubble stage could contribute to balancing soil nutrients and maintaining soil ecological function to a certain extent, but there may still be a risk of fungal disease.

Knowledge on microbial community shifts during ecosystem succession from bare surfaces resulting from massive landscape stripping is extremely limited. Here we took advantage of an artificially created experimental catchment (6 ha) to assess structural and functional changes of microbial communities in ephemeral stream sediments and adjacent soils between 3 and 13 years after catchment construction. The catchment has since developed in undisturbed conditions, with major transformations in its morphology, hydrology and vegetation reflected by changes in microbial community structure and function. Initially dominated by cyanobacteria (42% of 16S rRNA reads in 2008 and 0.3% in 2018), the bacterial community shifted to an essentially heterotrophic composition within 10 years, when Alphaproteobacteria (12 vs 21%) and Planctomycetes (3 vs 16%), in particular, gained in importance. Similarly, Sordariomycetes (5% of ITS reads in 2008 and 27% in 2018) replaced Dothideomycetes (53 vs 14%) as the prevailing fungal class. Microbial respiration rates increased tenfold, from an average of 0.5–4.4 μg CO 2 g −1 DM h −1 , accompanied by an increase in potential enzyme activities. Seasonal patterns of microbial community functions were accentuated over a decade of catchment development, whereas structural community changes were less pronounced. Spatial variation of community composition also increased, with differences between soils and sediments intensifying over time. However, a striking disconnect between microbial community structure and function in 2008 had vanished by 2018. Thus, a decade of ecosystem succession resulted in fundamental shifts in microbial community structure and function, highlighting the intricate interplay between changing environmental conditions and microbial responses. • Re-connection of microbial community structure and function within a decade. • Shift in bacterial community composition from autotroph to heterotroph dominance. • Increased spatial heterogeneity of microbial communities during catchment succession. • Amplified seasonal variation in microbial function but not community structure.

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands. Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands. DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities. Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community. Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site. Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

Microcosms were setup to investigate the possible impact of copper exposure on bacterial community structure and function in sediments of Jiaozhou Bay, China, by culture-independent microbial ecological techniques and community-level physiological profiling. Bacterial 16S rDNA libraries indicated that proportion of the bacteria in phyla Chloroflexi and Acidobacteria decreased, but that of Gammaproteobacteria and Planctomycetes slightly increased in copper-treated sediment. Denaturing gradient gel profiles showed that bacterial communities in control and copper exposed sediments developed into different directions, while the copper exposure did not change the pattern of ammonia oxidizing bacterial community. Microbial community-level physiological profiling revealed an obvious response to copper dosage. The copper pollution caused an acute decrease of carbon utilizing ability as well as bacterial functional diversity; the number of culturable heterotrophic bacteria was reduced by 90%. This study demonstrated that high copper input would obviously reduce culturable bacterial counts and seriously impact bacterial community function in marine sediments.

Integrated soil-crop management (ISCM) has been shown as an effective strategy to increase efficiency and yield while its soil microbial community structure and function remain unclear. We evaluated changes in soil physicochemical factors, bacterial community structure responses, and the contributions of soil properties and bacterial communities to summer maize-winter wheat yield and GHG emissions through an ISCM experiment [T1 (local smallholder farmers practice system), T2 (improved management system), T3 (high–yield production system), and T4 (optimized management system)], which could provide scientific guidance for sustainable development of soil in summer maize-winter wheat rotation system. The results showed that the optimized ISCM could improve the soil quality, which significantly changed the soil bacterial community structure to reduce GHG emissions and increase yield. The co-occurrence network density of T3 was increased significantly. The Acidobacteria (class) and OM190 (class) were enriched in T2 and T4. The Frankiales (order) and Gaiellales (order) were enriched in T3. However, the changes in different crop growth stages were different. At the wheat jointing stage and maize mature stage, T4 could enhance carbon-related functional groups, such as aromatic hydrocarbon degradation and hydrocarbon degradation, to increase the soil organic carbon content. And at the maize tasseling stage, T4 could enhance nitrogen-related functional groups. And soil bacteria structure and function indirectly affected annual yield and GHG emission. T2 and T4 exhibited a similar soil microbial community. However, the yield and nitrogen use efficiency of T2 were reduced compared to those of T4. The yield of T3 was the highest, but the GHG emission increased and soil pH and nitrogen use efficiency decreased significantly. Therefore, T4 was a suitable management system to improve soil quality and soil bacterial community structure and function to decrease GHG emissions and increase the yield of the summer maize-winter wheat rotation system.

Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites’ gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40–58 %), Spirochaetes (10–70 %), Firmicutes (17–27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28–45 %), Actinobacteria (20–40 %) and Proteobacteria (18–24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1262-6) contains supplementary material, which is available to authorized users.

In many urban catchments, the discharge of effluents from wastewater treatment plants (WWTPs), as well as untreated wastewaters (UWWs), presents a major challenge for the maintenance of river sediment and water quality. The discharge of these effluents cannot only increase the concentration of metals, nutrients and organic compounds in fluvial ecosystems, but also alter the abundance, structure and function of river bacterial communities. Here, we present data on chemical and biological quality parameters in wastewater-impacted and non-impacted river surface sediment and water samples. Overall, the concentration of nutrients (inorganic nitrogen) and some heavy metals (Zn, Ni and Cr) was positively correlated with the nirS/16S rRNA ratio, while nirK- and nosZ-denitrifier populations were negatively affected by the presence of ammonium in sediments. Bacterial community structure was significantly correlated with the (i) combined influence of nutrient and metal concentrations, (ii) the contamination level (non-impacted vs. impacted sites), (iii) type of contamination (WWTP or UWW), and (iv) location of the sampling sites. Moreover, the higher abundance of five genera of the family Rhodocyclaceae detected in wastewater-impacted sites is also likely to be an effect of effluent discharge. The data presented here complement a broader study (Martínez-Santos et al., 2018) [1] and they are particularly useful for those interested in understanding the impact of wastewater effluents on the abundance, structure and function of river bacterial communities involved in nitrogen cycling.

BackgroundThe planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem.MethodsHigh-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure.ResultsS. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors.ConclusionsEcological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community.

Interactions between quorum sensing/quorum quenching and virulence genes may affect coral health by regulating symbiotic bacterial community

The impacts of rice varieties with stacked drought tolerance and insect resistance on soil microbiomes are poorly understood. Hence, the objective of this study was to investigate the effects resulting from the cultivation of the drought-tolerant and insect-resistant rice cultivar, Hanhui3T, on soil physical–chemical properties, and bacterial and fungal community composition. Soil samples of Hanhui3T and conventional rice varieties (Hanhui3 and Zhonghua11) were collected in triplicate at the booting stage, and bacterial and fungal population sizes and community structures were assessed using qPCR and Illumina MiSeq sequencing, respectively. The Bt protein concentration of Hanhui3T was significantly higher than that of Hanhui3 and Zhonghua11, while the pH of Hanhui3T was significantly lower. Bacterial population sizes and community composition were significantly different between Hanhui3T and Hanhui3 (or Zhonghua11), while no similar effects were observed for fungal communities. These differences suggest that the effect of Hanhui3T cultivation on bacterial community composition is stronger than the effect on fungal communities. Moreover, bacterial abundance was positively correlated to soil pH, while bacterial community structure variations were mainly driven by soil pH and Bt protein concentration differences. In conclusion, the abundances and structure of bacterial communities were altered in rhizosphere with Hanhui3T cultivation that changed soil pH and Bt protein concentrations, while fungal communities displayed no such responsiveness.