Variation In Bacterial Community Structure Research Articles

Different types of agricultural land use drive distinct soil bacterial communities

Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

Greater variation of bacterial community structure in soybean- than maize-grown Mollisol soils in responses to seven-year elevated CO2 and temperature

Changes in rhizodeposits of crops under elevated CO2 (eCO2) and elevated temperature (eT) may substantially impact on soil microbial community, which in turn affects soil carbon and nutrient cycling. However, the responses of soil bacterial community to long-term eCO2 and eT are not fully understood. A seven-year field experiment using open-top chambers was carried out with soybean (Glycine max L. Merr.) and maize (Zea mays L.) grown in a Mollisol soil under ambient CO2 (380 ppm), eT (2.1 °C increase in air temperature) and eTeCO2 (elevated temperature plus elevated CO2, 2.1 °C increase in air temperature and 700 ppm CO2). Soil DNA was extracted for Illumina MiSeq sequencing. The principal coordinate analysis showed that changes of bacterial community structure due to eT and eTeCO2 were greater in soybean- than maize-grown soils. The eT increased the relative abundances of Gaiella and Bacillus in Actinobacteria and Firmicutes, but decreased those of Nocardioides and H16 in Actinobacteria and Proteobacteria, respectively. The magnitudes of responses of seven genera sensitive to eT varied between soybean- and maize-grown soils. The eTeCO2 decreased the relative abundance of Bacillus and increased those of Gaiella, Streptomyces and Mizugakiibacter. The abundances of Gaiella, Gemmatimonas, and Mizugakiibacter under eTeCO2 were higher in soybean- than maize-grown soils. The redundancy analysis showed that soil organic C, moisture, nitrate, microbial biomass N and Olsen-P significantly affected soil bacterial community composition. All these results indicate that long-term eT increased the abundance of bacterial community and shifted their composition compared to the ambient control. In addition, the bacterial community composition under eTeCO2 was more stable in maize- than soybean-grown soils. The study suggests that warming and crop species may interactively affect the stability of bacterial community linking to the sustainability of soil eco-function in future cropping systems.

Habitat and seasonal variations in bacterial community structure and diversity in sediments of a Shallow lake

Benthic bacteria are drivers of aquatic ecosystem material circulation and energy flow, and are sensitive to environmental changes. In this study, a total of 79 sediment samples were collected from four representative habitat types (duck farm, fish farm, lotus pond and residential area) and one reference site (conservation district) of Baiyangdian Lake, North China, in three seasons (winter, spring and summer). The physical and chemical properties and the levels of contaminants in sediment were determined. Bacterial communities were studied by 16S rRNA high-throughput sequencing techniques. The result showed that, Proteobacteria, Chloroflexi, Bacteroidetes, Firmicutes and Actinobacteria were the dominant species at the phylum level in Baiyangdian. Sulfuricurvum, Thiobacillus Dechloromonas, Sulfurovum, Nitrospira and Desulfatiglans were the dominant species at the genus level. The dominant genus was different among different habitats. Proteobacteria exhibited the highest relative abundance in all seasons, and the relative abundance of dominant bacteria was highest in winter. The main functional group from the sampling sites were contamination tolerance bacteria, such as sulfur-oxidizing, sulfate-reducing and nitrifying bacteria. Sulfur-oxidizing bacteria were found mainly in duck farms and residential areas, whereas sulfate-reducing bacteria and nitrifying bacteria occurred in lotus ponds. Habitat type was the most important factor influencing the bacterial community composition, evenness and diversity. Sediment pH and the amount of active phosphorus played the most important role in the composition of the bacterial community, and the heavy metals (Zn, Mn and Cr) and organic pollutants (polycyclic aromatic hydrocarbons, PAH) also had moderate influence. As Baiyangdian Lake is the central of Xiong’an New Area, the water quality management has become the hottest topic. Plenty of researches about environmental variables and aquatic species were taken, but lacking report of bacteria. This study provide basic information of bacterial community composition in this area, and help to understand the response of the bacterial community to habitat and seasonal change, which provide a scientific basis for the recovery and reconstruction of the degraded ecosystem.

Spatial variation in bacterial biomass, community composition and driving factors across a eutrophic river

Eutrophication is a global problem, and bacterial diversity and community composition are usually affected by eutrophication. However, limited information on the ecological significance of bacterial community during algae blooms of rivers has been given, more studies should be focused on the bacterial diversity and distribution characteristics in eutrophic rivers. In this study, we explored the spatial variations of bacterial biomass, community structure, and their relationship with environmental factors in the eutrophic Xiangxi River. The content of Chlorophyll (Chl) was about 16 mg/L in the midstream (S2, S3), which was in the range of light eutrophication. Significant spatial variation of bacterial community structure was found at different sites and depths (p < 0.05), and the driving environmental factor was found to be nitrogen, mainly detected as total nitrogen (TN), Kjeldahl nitrogen (KN), and ammonia nitrogen (NH4+) (p < 0.05). The midstream sites had some significantly different bacteria, including algicidal bacteria and dominant lineages during algal blooms. This result was consistent with the functional prediction, where significant higher abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was associated with algicidal substances in the midstream. At different water depths, some populations adapted to the surface layer, such as the class Flavobacteriia, and others preferred to inhabit in the bottom layer, such as Betaproteobacteria and Acidobacteria. The bacterial biomass was higher in the bottom layer than that in the surface and middle layer, and temperature and pH were found to be the major driving factors. The bacterial diversity increased with the increasing of depths in most sampling sites according to operational taxonomic units (OTUs), Chao1 and ACE indexes, and PO43− was demonstrated to be the most significant factor. In summary, this study offered the evidence for microbial distribution characteristics across different sites and depths in summer, and its relationship with environmental variables in a eutrophic river.

Response of Heterotrophic Bacteria Abundance and Community Structure to Asian Dust Addition in the Oligotrophic Northwest Pacific Ocean

The dust storms from the continent usually affect the abundance and diversity of planktons by supplying trace elements. As such, the response of heterotrophic planktonic bacteria to dusts, nutrients ( i.e. , nitrogen and phosphorus) or ferrous dosages was investigated in the Kuroshio Extension region of the Northwest Pacific Ocean (NWPO) through on-board incubation experiments during an oceanographic survey in spring 2014. The flow cytometry and 16S rRNA high-throughput sequencing methods were applied to explore the abundance and community structure of bacteria, and the percentage of high nucleic acid bacteria (HNA%). The results showed that the heterotrophic bacteria abundance was low (average 2.55 × 10 5 cells mL −1 ) and subjected to both nitrogen (N) and ferrous (Fe) limitation. Sand-dust deposition observably promoted the activity of heterotrophic planktonic bacteria. The maximum abundance of heterotrophic bacteria was 6.98 × 10 5 cells mL −1 in the dust-dosage group, which was 44% higher than the control ( P < 0.05). The HNA% in the dust-dosage group was 1.37 times higher than the control ( P < 0.05). The activation mechanism was mainly related to the dissolution of N and Fe in the dusts. The relative abundance of genus Winogradskyella was significantly increased by dust deposition while the relative abundance of the genera Tenacibaculum and Hyphomonas was decreased. These variations of bacterial community structure were ascribed to the dissolution of nutrients N and P. Comparing the results of different experimental groups, this study concluded that dust storm improved the abundance of heterotrophic bacteria by dissolution of N and Fe.

Variations in bacterial community structures during geothermal water recharge-induced bioclogging

Characterizing bacterial communities is of great significance for targeted control of bacteria-induced clogging during geothermal water recharge. Based on a series of laboratory-scale percolation experiments, the variations in bacterial community diversity, composition, and structure were investigated during simulated geothermal water recharge using high-throughput sequencing technology. The Chao, Shannon, and Evenness indexes were used to quantify the richness, diversity, and evenness of the bacterial community, respectively. The results show that the richness of the bacterial community initially increased and then decreased in the sand columns during the experiments of geothermal water recharge, while the changes in bacterial diversity and evenness were not apparent. A variety of bacterial phyla were found, among which Proteobacteria was predominant (88.31%), followed by Actinobacteria, Bacteroidetes, and Firmicutes (4.23%, 3.44%, and 2.49%). For the non-Proteobacterial phyla, Actinobacteria gradually disappeared while Bacteroidetes and Firmicutes were detected during the percolation experiments. This study implies that, despite the variations in the bacterial community, a core group of bacteria persists during geothermal water recharge, and thus a targeted control of bacteria-induced clogging during geothermal water recharge should be feasible.

Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields

Soil microorganisms are critical factors of plant productivity in terrestrial ecosystems. Coptis chinensis Franch is one of the most important medicinal plants in China. Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. In the current study, we provide detailed information regarding the diversity and composition of the rhizospheric bacterial communities of the C. chinensis plants in continuously cropped fields and fallow fields in two seasons (i.e., winter and summer) using next-generation sequencing. The alpha diversity was higher in the five-year cultivated C. chinensis field (CyS5) and lower in fallow fields (NCS). Significant differences analysis confirmed more biomarkers in the cultivated field soil than in fallow fields. Additionally, the principal coordinate analysis (PcoA) of the beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Besides, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the top bacterial phyla. Among these phyla, Proteobacteria were found predominantly and showed a decreasing trend with the continuous cropping of C. chinensis. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the abundance of C and N functional genes had a significant difference between the soil samples from cultivated (CyS1, CyS3, and CyS5) and fallow (NCS) fields in two seasons (winter and summer). The principal coordinate analysis (PCoA) based on UniFrac distances (i.e., unweighted and weighted) revealed the variations in bacterial community structures in the soil samples. This study could provide a reference for solving the increasingly severe cropping obstacles and promote the sustainable development of the C. chinensis industry.

Effect of Maize Straw Biochar on Bacterial Communities in Agricultural Soil.

Biochar has become a popular soil amendment. However, its effect on soil microbial community is still unclear. In the present study, maize straw biochar was pyrolysed at 300°C, 450°C and 600°C, respectively, and then was added to agricultural soil at the ratio of 0.5%, 1% and 2%. Bacterial dynamics was analyzed in the pot experiments using denaturing gradient gel electrophoresis. The results indicated that the pyrolysis temperature has great impact on the elemental composition, pH and porous structures of biochar. Moreover, pyrolysis temperature was primary factor to drive the variation of bacterial community structure in biochar amended soil. In addition, the results suggested that biochar amendments on agricultural soil would decrease the bacterial diversity, and selectively promote growth of functional bacteria to become the dominant community, which could increase the bacterial community organization and improve the stability of bacteria to counteract effects of perturbation.

Effect of different ecological treatment methods on microbial community in black and odorous sediment of urban river

底泥细菌代谢是城市河道底泥代谢物的主要来源，最终决定城市河道的生态状况.本文研究了黑臭河道底泥经添加硝酸钙、生物促生剂和种植沉水植物处理后底泥中细菌群落结构的响应，以期为城市黑臭河道细菌群落的改善和综合治理提供理论依据.实验结果表明：经过不同生态处理后，上覆水中，添加硝酸钙组总氮（TN）含量显著高于对照组，添加生物促生剂组溶解氧浓度显著高于对照组.沉积物中，所有处理组的氧化还原电位值（ORP）均显著高于对照组，种植沉水植物组和添加硝酸钙组TN含量均显著低于对照组，沉积物理化性质得到一定改善.对不同生态处理组底泥细菌群落的研究发现，处理组底泥细菌群落产生了较大变化，且不同处理组细菌群落变化不同，生物促生剂组底泥中细菌的Sobs指数和Chao 1指数显著高于对照组和硝酸钙组，且生物促生剂组Shannon指数和PD指数显著高于硝酸钙组.Proteobacteria（Deltaproteobacteria、Betaproteobacteria、Gammaproteobacteria）、Chloroflexi、Firmicutes、Bacteroidetes和Spirochaetae是各实验组的主要优势菌门；非度量多维尺度分析表明：硝酸钙和生物促生剂的投加可明显改变底泥细菌群落结构组成.在属水平上，uncultured_Anaerolineaceae、Ferribacterium、uncultured_Xanthomonadales_Incertae_Sedis是导致底泥细菌群落发生变化的主要菌属.冗余分析结果表明，底泥ORP的变化是驱动细菌群落结构变化的关键环境因素.;Sediment microorganisms are the main source of sediment metabolism in urban rivers, which ultimately determine the ecological status of the rivers. In this paper, to analyze the effect of different ecological treatments on sediment microbial community, we established artificial mesocosms to mimic sediment status of the black-stinking river with different ecological treatments as calcium nitrate, bio-energizer addition, and submerged macrophytes transplantation. Illumina Miseq sequencing was applied to reveal the bacteria community variations of all treated and untreated sediments. The results showed that in the overlying water, the total nitrogen (TN) content of calcium nitrate addition group was significantly higher than that in the control group, dissolved oxygen concentration in the bio-energizer addition group was significantly higher than that in the control group. In the sediment, the oxidation reduction potential (ORP) values of all the treatment groups were significantly higher than those in the control group; TN content of calcium nitrate addition group and submerged macrophytes transplantation group were both significantly lower than those in the control group, which indicate the improvement of sediment status of treatment group. Bacterial communities were also varied in treatment group, and showed diverse variations with different treatments. The Sobs and Chao 1 microbial diversity indices in the bio-energizer addition group were both significantly higher than those in the control group and calcium nitrate addition group; the Shannon and PD diversity indices for microbes in the bio-energizer addition sediment were both significantly higher than those in calcium nitrate addition group. All sediment microbial communities were dominated by Proteobacteria (Deltaproteobacteria, Betaproteobacteria, Gammaproteobacteria), Chloroflexi, Firmicutes, Bacteroidetes and Spirochaetae phyla. Nonmetric multidimensional scaling analysis showed that the addition of calcium nitrate and bio-energizer can significantly alter the composition of bacterial community structure. Uncultured_Anaerolineaceae, Ferribacterium and uncultured_Xanthomonadales_Incertaeae_Sedis were the main genus causing variations in the bacterial community. Redundancy analysis indicated that the change of sediment ORP is a key environmental factor driving the variation of bacterial community structure.

Divergent responses of soil bacterial communities in erosion-deposition plots on the Loess Plateau

Soil erosion and deposition occur widely from regional to global scales and have profound impacts on ecological services and sustainability. Despite their crucial roles in biogeochemical cycles, the responses of soil bacterial communities to soil erosion and deposition remain largely unclear. In this study, a field simulation experiment was conducted to examine variation in soil bacterial communities across eroding slopes and depositional zones with three slope gradients (5°, 10° and 20°) on the Loess Plateau of China (2015–2017). The results showed that soil physicochemical properties were altered by redistribution of runoff and sediment across eroding slopes and depositional zones. Soil bacterial alpha diversity was higher in the depositional zones of both 10° and 20° slopes compared with the 5° reference slopes but no markedly difference was found between eroding slopes and reference slopes. By contrast, bacterial community structure differed between eroding slopes and reference slopes but not between depositional zones and reference slopes. Differentiation of bacterial communities between eroding slopes and depositional zones increased with increasing slope gradients. The bacterial network was greater and more complex within depositional zone than eroding slope, indicating more extensive bacterial interactions and greater community stability potential. Erosion- and deposition-induced redistribution of soil moisture, soil organic matter, available P, and available K were the key determinants of variation in bacterial community structure. Our findings demonstrate the contrasting effects of soil erosion and deposition on soil bacterial communities, which should be given further attention across eroding landscapes.

The spatial and seasonal variations of bacterial community structure and influencing factors in river sediments

Studying the composition and structure of bacterial communities in sediments helps to understand the contribution of bacteria to environmental changes and the role of feedback in response to disturbances. However, seasonal changes in bacterial communities of river sediments with different pollution levels and sources have not been clear yet. In this study, we collected sediment samples during the dry season, wet season and level season from 40 sites with various pollution sources in three inflow rivers (Fengle-Hangbu River, Nanfei River and Zhegao River) of Chaohu Lake. Bacterial community compositions were determined based on high-throughput sequencing. The ‘Bioenv’ in the R package ‘Vegan’ and redundancy analysis was used to explore the influence of environmental factors on the bacterial community in the river sediments. Results showed that a significant deviation in bacterial communities was found among seasons and rivers. In addition, seasonal dynamics had a greater impact on shaping bacterial communities than rivers with different pollution sources. A higher diversity was found in the wet season as compared to the other seasons. The bacterial diversity was negatively correlated with nutrients (OM, TN, NH4+, IP, OP and TP) and metals (Cu and Zn). Bacterial communities were more sensitive to heavy metals pressure than nutrients. We also concluded that heavy metals (Cu and Cd) were the key contributing factors in explaining variations in bacterial communities. This study provided a valuable reference for assessing ecological stress.

Sharp contrasts between freshwater and marine microbial enzymatic capabilities, community composition, and DOM pools in a NE Greenland fjord

AbstractIncreasing glacial discharge can lower salinity and alter organic matter (OM) supply in fjords, but assessing the biogeochemical effects of enhanced freshwater fluxes requires understanding of microbial interactions with OM across salinity gradients. Here, we examined microbial enzymatic capabilities—in bulk waters (nonsize‐fractionated) and on particles (≥ 1.6 μm)—to hydrolyze common OM constituents (peptides, glucose, polysaccharides) along a freshwater–marine continuum within Tyrolerfjord‐Young Sound. Bulk peptidase activities were up to 15‐fold higher in the fjord than in glacial rivers, whereas bulk glucosidase activities in rivers were twofold greater, despite fourfold lower cell counts. Particle‐associated glucosidase activities showed similar trends by salinity, but particle‐associated peptidase activities were up to fivefold higher—or, for several peptidases, only detectable—in the fjord. Bulk polysaccharide hydrolase activities also exhibited freshwater–marine contrasts: xylan hydrolysis rates were fivefold higher in rivers, while chondroitin hydrolysis rates were 30‐fold greater in the fjord. Contrasting enzymatic patterns paralleled variations in bacterial community structure, with most robust compositional shifts in river‐to‐fjord transitions, signifying a taxonomic and genetic basis for functional differences in freshwater and marine waters. However, distinct dissolved organic matter (DOM) pools across the salinity gradient, as well as a positive relationship between several enzymatic activities and DOM compounds, indicate that DOM supply exerts a more proximate control on microbial activities. Thus, differing microbial enzymatic capabilities, community structure, and DOM composition—interwoven with salinity and water mass origins—suggest that increased meltwater may alter OM retention and processing in fjords, changing the pool of OM supplied to coastal Arctic microbial communities.

Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling.

The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts.

Spatiotemporal Controls on the Urban Aerobiome

Greater exposure to environmental microorganisms has been hypothesized to reduce the likelihood of developing autoimmune disorders, and vegetation is known to be a source of diverse microbiota to the air. However, the spatiotemporal dynamics of airborne microbial communities in urban environments with varying amounts and types of vegetation are poorly understood. In this study we used high-throughput sequencing of the bacterial 16S rRNA gene to assess whether fine-scale variation in urban vegetation influences the diversity, composition, or structure of airborne bacterial communities over time. We used passive settling dishes to collect airborne bacteria from 36 sites representing three urban land cover types (forest, grassland, paved) over a 3-month period in Eugene-Springfield, Oregon, USA. We used remote sensing data (aerial 4-band orthoimagery and LiDAR) and geographic information systems (GIS) to assess detailed site characteristics (e.g., total vegetation cover and structural diversity) for each site. Our initial analysis indicated that site was the most important factor explaining variation in bacterial community structure (R2 = 0.32, p < 0.001), followed by sampling date (R2 = 0.24, p < 0.001), while land cover type was a significant but weak predictor (R2 = 0.06, p < 0.001) and other vegetation metrics were even less predictive. However, when samples were analyzed separately by date, the explanatory power of land cover type increased substantially; six of nine dates showed significant effects (p < 0.05) with R2 ranging from 0.16–0.31, indicating that land cover type had a marked influence on bacterial community structure that was obscured by the effects of site and sampling date. Despite the importance of site as a predictor of bacterial community structure, Mantel tests for spatial correlation were insignificant for most sampling dates, suggesting that localized site characteristics were driving this relationship. We use our results to propose a space-time conceptual model of the interactions between site-scale environmental features (e.g., vegetation characteristics) and regional-scale temporal processes and events (e.g., agricultural harvesting) to understand and perhaps manage intraurban airborne bacterial communities.

Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands.

Coastal ecosystems experience some of the most active land–ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.

Effect of biochar origin and soil type on the greenhouse gas emission and the bacterial community structure in N fertilised acidic sandy and alkaline clay soil

Soil amendment with biochar has received increased attention because of its potential to i) sequester carbon and ii) reduce N2O emission when applied to N fertilised soils. To study the effect of biochar origin on greenhouse gas emission in two contrasting soil types, we used a robotized continuous flow incubation system and δ13C stable isotope approach to compare four biochar types (feed stock: olive mill, corn cob, pistachio shell, cotton stalk) in an alkaline clay soil and two selected biochar types (feed stock: olive mill and corn cob) in an acidic sandy soil. Furthermore, high-throughput sequencing of 16S rRNA genes was performed at the end of the incubation to investigate the effect of different biochars on bacterial community structure in the two different soils. In the alkaline clay soil, all biochar types in conjunction with N fertiliser decreased CO2 emissions up to 12% compared to the N added control treatment causing negative priming, whereas no significant effect of biochar addition on N2O emissions was observed. In contrast, application of olive mill biochar to the acidic sandy soil significantly increased soil pH, CO2, and N2O fluxes, whereas no significant effect of corn cob biochar addition was observed. There was a significant linear relationship between the biochar induced increase in soil pH and the biochar induced increase in soil born N2O emission. Additionally, we detected a clear variation in bacterial community structure in the acidic sandy soil (phyla Acidobacteria, Nitrospirare, and Arthrobacter) with the olive mill biochar addition. Overall, the amendment of different biochars failed to mitigate N2O emissions in both soil types when mineral fertiliser was added. Furthermore, amendment of olive mill biochar stimulated both N2O and CO2 emissions in the low pH sandy soil and altered the bacterial community structure, which was possibly related to its liming effect.

Effects of 7 years experimental warming on soil bacterial and fungal community structure in the Northern Tibet alpine meadow at three elevations

A warming experiment was established along an altitudinal gradient (low elevation: 4313 m, mid-elevation: 4513 m and high elevation: 4693 m) in alpine meadows of the Northern Tibet to investigate the effects of warming on soil bacterial and fungal community structure. Elevation had significant effects on vegetation community coverage (CC), soil temperature (Ts) and pH, but not soil fungal diversity. Soil bacterial diversity at the high elevation was significantly lower than that at the low and mid-elevations, whereas there was no significant difference of soil bacterial diversity between the low and mid-elevations. After seven years of warming, soil fungal diversity was significantly increased at the mid-elevation but not the low and high elevations, and soil bacterial diversity was not significantly altered at the low, mid- and high elevations. Soil bacterial community structure was significantly altered at the low and mid-elevations but not the high elevation. Soil fungal community structure was significantly altered at all the three elevations. CC, Ts and pH significantly explained 20.55%, 5.30% and 12.61% of the variation of bacterial community structure, respectively. CC and Ts significantly explained 17.40% and 5.86% of the variation of fungal community structure, respectively. Therefore, responses of soil microbial community structure to warming may vary with elevation, which was mainly attributed to different vegetation coverage, soil temperature and/or pH conditions among the three elevations in this study alpine meadows.

The Biogeographical Distribution of Soil Bacterial Communities in the Loess Plateau as Revealed by High-Throughput Sequencing

The rigorous environmental stress of the severely eroded Loess Plateau may have promoted specific soil bacterial communities in comparison to other eco-environmental regions. In order to unmask the bacterial diversity and most influential environmental parameters, Illumina MiSeq high throughput sequencing of 16S rRNA from 24 representative soil samples collected across south-east to north-west transect of the Loess Plateau in northern Shaanxi, China was conducted. This high-throughput sequencing revealed a total of 1,411,001 high quality sequences that classified into 38 phyla, 127 classes, >240 orders, and over 650 genera, suggesting a high bacterial richness across the Loess Plateau soils. The seven dominant groups were: Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, and Verrucomicrobi (relative abundance of >5%). Increasing/decreasing soil pH and geographic longitudinal distance correlated significantly with increasing/decreasing bacterial richness and diversity indices. Pairwise correlation analysis showed higher bacterial diversity at longitudinal gradients across 107°39′-109°15′ (south-east to north-west) in our studied Chinese loess zone. Variation partitioning analysis indicated significant influence of soil characteristics (~40.4%) than geographical distance (at a landscape scale of ~400 km) that was responsible for 13.6% of variation in bacterial community structure from these soils. Overall, contemporary soil characteristics structure the bacterial community in Loess Plateau soil to a greater extent than the spatial distances along the loess transect.

Variation in the Soil Microbial Community of Reclaimed Land over Different Reclamation Periods

Improvement of soil quality after land reclamation is a key concern in mining areas. However, the characteristics and internal mechanisms of variation of bacterial community structure over different reclamation periods are currently unclear. The recovery and evolution of soil microbial community structure are important indicators of the level of soil quality improvement of reclaimed soil. Therefore, this study investigated soil samples from coal gangue-filled land after reclamation periods of 1, 6, and 15 years. To accomplish this, 16S rRNA gene libraries were produced to determine the microbial community composition of the soils. In addition, various soil microbial community characteristics in the filled reclamation areas were compared with soil samples from areas unaffected by coal mining. The results showed the following: (1) The diversity and abundance of bacterial communities in reclaimed soils was slightly different from that of natural soils. However, the soil bacterial community structure was highly similar to natural soil after a 15-year reclamation period; therefore, the recovery of bacterial communities can be used as an indicator of the effects of rehabilitation. (2) Some soil physicochemical properties are significantly correlated with the main bacteria in the soil. (3) The dominant bacteria included members of the phyla Firmicutes and Proteobacteria, as well as members of the genera Bacillus, Enterococcus, and Lactococcus. Taken together, the results of this study indicated that the application of microbial remediation technology can be used to adjust the soil microbial community structure, improve soil quality, and shorten the soil recovery period.

Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem.

Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.