Copiotrophic Groups Research Articles

Alpine meadow degradation decreases soil P availability by altering phoD-harbouring bacterial diversity

Context Soil degradation is usually accompanied by significant changes in phosphorus (P) availability, which complicates soil management. However, the effect of ecosystem degradation on soil P availability remains poorly understood, especially in the alpine ecosystem, which is one of the most understudied and vulnerable terrestrial habitats of the planet. Aims Assess the effect of meadow degradation on soil P availability in the alpine ecosystem. Methods Changes in soil P-related properties, phoD-harbouring bacterial communities, and alkaline phosphatase levels were investigated in four alpine meadows along a degradation gradient (non-degraded, lightly degraded, moderately degraded, and severely degraded) on the Tibetan Plateau. Key results We found meadow degradation reduced alkaline phosphatase activity by 6.3–11.22% and soil P availability by 27.1–42.4% compared to the respective values in the non-degraded meadows, but this negative impact was only observed in moderately and severely degraded meadows. Meadow degradation caused a P limitation on the phoD-harbouring community and a decline in the abundance of phoD genes and diversity of phoD-harbouring bacterial communities, with an increase in oligotrophic groups (e.g. Actinobacteria) and a reduction in copiotrophic groups (e.g. Proteobacteria). The degradation-induced reduction in soil C supply and plant biomass decreased soil P availability by lowering the activity of alkaline phosphatases, which are closely associated with phoD-harbouring bacterial structure and diversity. Alloactinosynnema and Actinomadura were identified as the key taxa contributing to alkaline phosphatases activity. Conclusions Alpine meadow degradation decreases soil P availability by altering phoD-harbouring bacterial diversity. Implications Our results revealed the mechanisms of decreased P availability during alpine meadow degradation, which can guide the restoration of degraded meadow ecosystems.

Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere

Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.

Exploitation alters microbial community and its co-occurrence patterns in ionic rare earth mining sites

The exploitation of ion-adsorption rare earth elements (REEs) deposits results in serious ecological and environmental problems, which has attracted much attention. However, the influences of exploitation on the prokaryotic communities and their complex interactions remain poorly understood. In the present study, bacterial and archaeal communities, as well as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), in and around REEs mining area were investigated through high throughput sequencing and quantitative polymerase chain reaction (qPCR). Our results indicated that mining soil was characterized by poor soil structure, nutrient deficiency, and high concentrations of residual REEs. Oligotrophic bacteria (e.g., Chloroflexi and Acidobacteriota) were dominant in unexploited soil and mining soil, while copiotrophic bacteria (Proteobacteria and Actinobacteriota) were more abundant in surrounding soil. Nutrient was the key factor affecting microbial variation and abundance in mining soil. The bacterial community was more sensitive to REEs, while the archaeal communities were relatively stable. As the key members for ammonia oxidation, AOA outnumbered AOB in all the soil types, and the former was significantly influenced by pH, nutrients, and TREEs in mining soil. The microbial co-occurrence network analysis demonstrated that exploitation significantly influenced topological properties, decreased the complexity, and resulted in a much unstable network, leading to a more fragile microbial ecosystem in mining areas. Notably, the abundance of keystone taxa decreased after exploitation, and oligotrophic groups (Chloroflexi) replaced copiotrophic groups (Proteobacteria and Actinobacteriota) as the key to rebuilt a co-occurrence network, suggesting potentially important roles in maintaining network stability. The current results are of great significance to the ecological risk assessment of REEs exploitation.

Soil microbial community and their functional genes during grassland restoration

Soil microbial functional genes are linked with carbon (C) as well as nitrogen (N) cycling processes, and their relative abundances are strongly affected by ecosystem managements. Yet, soil microbial community compositions and their C, N cycling genes’ abundance in temperate grasslands remain poorly studied. Here, the Illumina MiSeq sequencing (16 S rRNA gene and internal transcribed spacer [ITS]) and meta-genomic GeoChip sequencing technologies were used to explore the alterations of microbial compositions and functional genes in the topsoil (0–10 cm) following grassland restoration. Grassland restoration increased the relative abundances of the copiotrophs (such as Actinobacteria, Proteobacteria, Bacteroidetes), but reduced the oligotrophs (including Acidobacteria, Chloroflexi, Planctomycetes), suggesting that microorganisms shifted from oligotrophic to copiotrophic groups during grassland restoration. The changes in microbial eco-strategies were also supported by the meta-genomic GeoChip sequencing data. In the early restoration years, the microbial functional genes were dominant with recalcitrant C degradation (pgu, glx, lig, mnp), C fixation (accA, aclB, acsA, rbcL), N fixation (nifH), and nitrification (amoA, hao) related genes. In the later restoration years, the microbial functional genes were dominant with labile C degradation (amyA, amyX, apu, sga, abfA), and denitrification (nosZ, nirS, narG, napA) related genes. The changes in microbial functional genes were mainly related to soil biotic factors (microbial biomass C and N, as well as C- and N-acquiring enzymes). Finally, we made a framework illustrating the changes in microbial eco-strategies and soil C, N cycling processes. This is the first attempt to link microbial functional genes with microbial eco-strategies by incorporating soil microbial meta-genomic information during grassland restoration.

Importance of soil labile organic carbon fractions in shaping microbial community after vegetation restoration

Studies have been increasingly focusing on soil carbon (C) pools to facilitate the sequestration and stabilisation of soil organic carbon (SOC). However, interactions between different SOC fractions and microbial communities have remained largely unexplored after vegetation restoration on the Loess Plateau. To address this gap, we analysed 16S and ITS rRNA gene sequencing, active SOC (Ca), slow SOC (Cs), passive SOC (Cp) and edaphic factors to decipher the importance of soil C fractions in shaping microbial communities after vegetation restoration. Compared to CK (Control, cropland), the average of SOC contents improved 70.52 % (p < 0.05), and the Ca, Cs and Cp improved 83.18 % (p < 0.05), 128.74 % (p < 0.05) and 18.69 % (p > 0.05). Under different land use types, the relative abundance of four bacterial phyla and two fungal phylum were > 80 % and 75 %, respectively. The Actinobacteria relative abundance in natural grassland and natural shrubland was higher than that in CK. The Shannon index, Chao index and OTUs of soil fungal and bacterial communities under CK were significantly lower than that of other land use types, except for artificial grassland (p < 0.05). The microbial communities transited from oligotrophic to copiotrophic groups according to the results of redundancy analysis (RDA), and the cumulative loads of two axes of RDA in bacterial and fungal communities approached 89.90 % and 88.19 %. The variation partitioning analysis showed that Ca and Cs exhibited large path coefficients in explaining the changes in soil microbial communities. And the microbial communities were mediated through change in labile organic C according to structural equation models, indicating that the structures and compositions of microbial communities were mainly under the control of labile SOC content after vegetation restoration. These results are referentially valuable for comprehending how to apply labile SOC in predicting variations of microbial communities and improving predictive ecosystem models for early-warning indicators of soil degradation.

Co-occurrence network of microbial communities affected by application of anaerobic fermentation residues during phytoremediation of ionic rare earth tailings area

The long-term exploitation of ionic rare earth elements (REEs) in southern China has produced a large-scale of abandoned tailings area. While the application of anaerobic fermentation residues to cultivate economically valuable remediation plants (e.g. energy plant) has become a hotspot due to their merits in low-cost and sustainability in recent years, the succession and co-occurrence patterns of these microbial communities remain unclear. In this study, soil samples were collected from the sustainable restoration area, natural restoration area and tailings area. The composition and diversity of bacterial and fungal communities on five soil samples were evaluated using high-throughput sequencing technology. The results shown that the phytoremediation with anaerobic fermentation residues could significantly improve the physicochemical properties (especially for soil nutrients) and microbial diversity of soil within 3 years, while these parameters in natural restoration area were lower. The nonmetric multidimensional scaling (NMDS) ordinations revealed the shifts of microbial communities depending on soil physicochemical properties and plant species, and soil nutrients were the main factors affecting the microbial variation explained by the variation partition analysis (VPA). The soil nutrient accumulation obviously changed the proportion of oligotrophic and copiotrophic groups, among which the copiotrophic groups were significantly increased, such as Proteobacteria, Bacteroidetes, Gemmatimonadetes and Glomeromycota. The microbial co-occurrence network analysis indicated that application of anaerobic fermentation residues could significantly improve the topological properties and the stability of microbial network. The copiotrophic groups (e.g. Proteobacteria, Ascomycota) became the key to assemble stable network structure. Moreover, herbaceous plants could increase the proportion of fungi (e.g. Ascomycota) in microbial network, which improved the topological properties with bacteria synergistically. Therefore, the soil environment of REEs tailings area was effectively optimized by anaerobic fermentation residues and herbaceous plants, which furthered understanding of co-occurrence pattern and mutualistic relationships of microbial communities during sustainable restoration.

Long-term excessive application of K2SO4 fertilizer alters bacterial community and functional pathway of tobacco-planting soil.

To improve tobacco leaf quality, excessive K2SO4 fertilizers were applied to soils in major tobacco-planting areas in China. However, the effects of K2SO4 application on soil microbial community and functions are still unclear. An eight-year field experiment with three kinds of K2SO4 amounts (low amount, K2O 82.57 kg hm-2, LK; moderate amount, K2O 165.07 kg hm-2, MK; high amount, K2O 247.58 kg hm-2, HK) was established to assess the effects of K2SO4 application on the chemical and bacterial characteristics of tobacco-planting soil using 16S rRNA gene and metagenomic sequencing approaches. Results showed that HK led to lower pH and higher nitrogen (N), potassium (K), sulfur(S) and organic matter contents of the soil than LK. The bacterial community composition of HK was significantly different from those of MK and LK, while these of MK and LK were similar. Compared to LK, HK increased the relative abundance of predicted copiotrophic groups (e.g. Burkholderiaceae, Rhodospirillaceae families and Ellin6067 genus) and potentially beneficial bacteria (e.g. Gemmatimonadetes phylum and Bacillus genus) associated with pathogens and heavy metal resistance, N fixation, dissolution of phosphorus and K. While some oligotrophic taxa (e.g. Acidobacteria phylum) related to carbon, N metabolism exhibited adverse responses to HK. Metagenomic analysis suggested that the improvement of pathways related to carbohydrate metabolism and genetic information processing by HK might be the self-protection mechanism of microorganisms against environmental stress. Besides, the redundancy analysis and variation partitioning analysis showed that soil pH, available K and S were the primary soil factors in shifting the bacterial community and KEGG pathways. This study provides a clear understanding of the responses of soil microbial communities and potential functions to excessive application of K2SO4 in tobacco-planting soil.

Contrasting response of soil N2O release to ammonium, nitrate, and urea addition rates is determined by substrate availability and microbial community abundance and composition

Although nonlinear responses of soil nitrous oxide (N2O) release to exogenous nitrogen (N) input have been reported, the contrasting effects of oxidized and reduced N forms and their driving mechanisms have rarely been investigated. Here, a 91-day microcosm incubation experiment with three forms (ammonium, nitrate, and urea) and eleven rates (0, 1, 2, 4, 6, 8, 10, 12, 14, 28, and 56 g N m−2 yr−1) of N addition was conducted to determine the response dose, saturation threshold, and turning point of N2O release from the temperate forest soil. Simultaneously, soil biochemical properties, N-cycling functional gene abundances, and bacterial and fungal community composition were determined to assess the biotic and abiotic contributions to changes in soil N2O release. The responses of soil N2O release rate to ammonium, nitrate, and urea addition rates exhibited saturation, sigmoidal, and exponential curves, respectively. The response dose of soil N2O release was higher in urea addition than in ammonium and nitrate additions (28 g N m−2 yr−1 vs. 8 g N m−2 yr−1). The tipping point and saturation thresholds for ammonium and nitrate additions were estimated to be 14 g N m−2 yr−1 and 56 g N m−2 yr−1, respectively, whereas neither occurred in urea addition. Except high rate of ammonium addition (≥28 g N m−2 yr−1), N inputs significantly increased AOB abundance and promoted soil NO3−-N accumulation. Also, N addition, especially high-rate ammonium, led to a shift in bacterial community from oligotrophic to copiotrophic groups. Oxidized nitrate input increased soil NO3−-N content and changed bacterial and fungal community structure, whereas reduced ammonium and urea additions increased soil NH4+-N content and AOB abundance, as well as altered bacterial community. These findings highlight that N forms contrastingly affect soil N2O release. Substrate availability, functional gene abundance, and microbial community composition equally contribute to soil N2O release, which should be considered in terrestrial ecosystem process models.

Microscale heterogeneity of soil bacterial communities under long-term fertilizations in fluvo-aquic soils

Differently sized soil aggregates, with non-uniform distribution of space and nutrients, provide spatially heterogeneous microenvironments for microorganisms and are important for controlling microbial community ecology and biogeochemistry in soils. Here, we investigated the prokaryotic communities within different aggregate-size fractions: macroaggregate (>0.25 mm), microaggregate (0.053–0.25 mm) and silt + clay (< 0.053 mm). These were isolated from fluvo-aquic soils under 39-year fertilization strategies: no fertilizer (CK), chemical fertilizer (NPK), manure fertilizer (M), and combination of manure and chemical fertilizers (MNPK). The results showed that the proportion of macroaggregate, soil aggregate-associated organic carbon (SOC) content and aggregate stability were all significantly increased by both manure and chemical fertilizations. Organic fertilizations (M and MNPK) more effectively boosted formation and stability of macroaggregates and enhanced SOC concentration than NPK. The distribution patterns of microorganisms in aggregates were primarily shaped by fertilization and aggregate size. They explained 76.9% of the variance in bacterial community compositions. Fertilizations, especially with organic fertilizers primarily transitioned bacterial communities from slow-growing oligotrophic groups (e.g., Chloroflexi) dominance to fast-growing copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) dominance across all aggregate sizes. Macroaggregates possessed a more stable bacterial community and efficiency of resource transfer, while smaller aggregates increased antagonism and weakened mutualism among bacterial communities. Overall, combination of manure and chemical fertilizers was crucial for increasing SOC content and aggregation, leading to a clear shift in bacterial community structures at aggregate scale.

Short-Term Effects of Cover Grass on Soil Microbial Communities in an Apple Orchard on the Loess Plateau

Grass cover may improve soil environmental conditions in apple orchards. However, the mechanisms for how the soil microbial community changes after cover grass treatments are not well understood. In this study, we analyzed soil properties, microbial community diversity and composition in an apple orchard after being covered with native wild grasses for 3 years on the Loess Plateau, China. The ratios of cover grass were 0% (no cover, NC), 20% (low-intensity cover, LIC), 40% (moderate-intensity cover, MIC1), 60% (moderate-intensity cover, MIC2) and 80% (high-intensity cover, HIC). Meanwhile, the relationships between soil nutrients, cover grass properties, and microbial communities was analyzed by redundancy analysis and Pearson correlations. The results showed that cover grass altered the bacterial community composition, and significant changes at the phylum level were mainly caused by Proteobacteria, Bacteroidetes and Chloroflexi. Compared with NC, the abundance of Proteobacteria was lower in LIC, and the abundance of Bacteroidetes was lower in LIC, MIC1 and MIC2, while that of Chloroflexi was higher in LIC. LIC and MIC1 were the only cover grass intensities that altered the soil fungal community composition; there were no significant differences at the phylum level. The changes in the soil microbial community at the given phyla may be related to the change in soil available nitrogen content caused by cover grass. Here, we demonstrate that cover grass changed the soil microbial community, and the changes may be attributed to the given phyla in the bacterial community; soil copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) were found to be at lower abundance in the low-intensity cover grass.

Linkage between soil ectoenzyme stoichiometry ratios and microbial diversity following the conversion of cropland into grassland

Soil ectoenzyme activities (mainly carbon [C]-, nitrogen [N]- as well as phosphorus [P]-acquiring enzymes) and their ratios are the sensitive indicators for the nutrients and energy demands for microbes. How ectoenzyme stoichiometry ratios mediate the changes in microbial community composition and diversity following the conversion of cropland into grassland remains unknown. This study assessed the effects of soil abiotic, biotic factors, and ectoenzyme stoichiometry ratios on microbial diversity (using high-throughput sequencing) following the conversion of cropland into grassland (Cropland and 5, 10, 15, 25, and 30 year natural successional grasslands). Soil ectoenzyme activities synchronously increased with the increase of bacterial and fungal alpha diversity following the conversion of cropland into grassland. Moreover, biotic and abiotic factors co-explained microbial diversity by the changes of ectoenzyme stoichiometry ratios. Specially, ectoenzyme stoichiometry ratios were strongly related to the relative abundance of predominant fungal phylum (Ascomycota, Basidiomycota) and bacterial phylum (Acidobacteria), and ultimately leading to the microbial life history strategies transiting from the oligotrophic groups with retarded growth, to the copiotrophic groups with rapid growth. These differences of microbial community composition, driven by ectoenzyme stoichiometry ratios, reflect soil microbial nutrient cycling following the conversion of cropland into grassland.

Crop type drives soil bacterial community and functional structure on the Loess Plateau terraces of China

Although terraced fields play an important role in soil and water conservation and agricultural production, the effects of planting different crops on the terraced soil bacterial community and functional structure are still unclear. We compared bacterial communities and functional structures in terraced soils grown with different crops on the Loess Plateau using the MiSeq technique. Economic crop types (apple [<i>Malus domestica</i>], greenhouse, intercropping), traditional crop types (corn [<i>Zea mays</i>], potato [<i>Solanum tuberosum</i>]), and terraced fields abandoned for five years in two small catchment areas in Ansai, Shaanxi, were selected, and the composition of the bacterial communities and other physicochemical properties of the soil were analyzed. The numbers of operational taxonomic units and bacteria α-diversity in economic and traditional crop types were 1.05 to 1.23 times higher than those in abandoned land; the change in crop types had significant effects on the soil bacterial community, and soil available phosphorus (P) content and bulk density were the main factors affecting the soil bacterial community. The dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Gemmatimonadetes, and the Proteobacteria accounted for 35% of the community in greenhouses but 30% in abandoned land. The co-occurrence networks indicated that economic crop types increased the links between soil bacterial taxa and the intensity of stability for terraced agroecosystems, especially for copiotrophic groups (Proteobacteria). Economic crop types enhanced potential functions of nitrogen (N) fixation and the carbon (C) cycle and reduced soil pathogens. These observations indicate that scientific planting and management could improve soil quality and health, which is conducive to sustainable agricultural development on the Loess Plateau terraces.

Soil prokaryotic community structure and co-occurrence patterns on the fragmented Chinese Loess Plateau: Effects of topographic units of a soil eroding catena

Soil prokaryotes composition and diversity are the key to uncovering the mechanisms that drive variations in soil biogeochemical processes. Soil erosion is a primary factor that affects the spatial distribution of the soil prokaryotic community, but how soil prokaryotes in soil-eroding catena respond to environmental factors related to topography remains largely unclear. In this study, topsoils were sampled from three typical erosion geomorphic units (autonomous, transitional and depositional zones) in 2018 to identify the soil prokaryotic community and interactions among the species on the Chinese Loess Plateau. The alpha-diversity was greater but the beta-diversity was lower in the autonomous and transitional zones than in the depositional zone. Gammaproteobacteria and Bacteroidetes were 73% and 68% lower in the autonomous and transitional zones than in the depositional zone. In addition, Deltaproteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Gemmatimonadetes and Nitrospirae were significantly higher in the autonomous and transitional zones. A less clustered network and fewer co-occurrences within the prokaryotic community and functional groups of processes were found in the depositional zone than in the autonomous and transitional zones. The alpha-diversity index was significantly negatively correlated with clay particles, soil water content, soil organic carbon (SOC), and ratio of SOC and nitrogen (C/N) but positively correlated with total nitrogen (TN). The higher relative abundances of copiotrophic groups (including Gammaproteobacteria, Bacteroidetes, etc.) in the depositional zone was mainly due to the increased SOC caused by the deposition of SOC-rich clay. Reassembly of the soil physico-chemistry characteristics among the topographic units significantly altered the soil prokaryotic community along the soil-eroding catena.

Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil.

ABSTRACTRecycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied total RNA sequencing to simultaneously assess the impact of wood ash amendment on the active soil microbial communities and the expression of functional genes from all microbial taxa. Wood ash significantly affected the taxonomic (rRNA) as well as functional (mRNA) profiles of both agricultural and forest soil. Increase in pH, electrical conductivity, dissolved organic carbon and phosphate were the most important physicochemical drivers for the observed changes. Wood ash amendment increased the relative abundance of the copiotrophic groups Chitinonophagaceae (Bacteroidetes) and Rhizobiales (Alphaproteobacteria) and resulted in higher expression of genes involved in metabolism and cell growth. Finally, total RNA sequencing allowed us to show that some groups of bacterial feeding protozoa increased concomitantly to the enhanced bacterial growth, which shows their pivotal role in the regulation of bacterial abundance in soil.

Microbial resistance promotes plant production in a four-decade nutrient fertilization experiment

There is a current lack of mechanistic understanding on the relationships between a soil microbial community, crop production, and nutrient fertilization. Here, we combined ecological network theory with ecological resistance index to evaluate the responses of microbial community to additions of multiple inorganic and organic fertilizers, and their associations with wheat production in a 35-year field experiment. We found that microbial phylotypes were grouped into four major ecological clusters, which contained a certain proportions of fast-growers, copiotrophic groups, and potential plant pathogens. The application of combined inorganic fertilizers and cow manure led to the most resistant (less responsive) microbial community, which was associated with the highest levels of plant production, nutrient availability, and the lowest relative abundance of potential fungal plant pathogens after 35 years of nutrient fertilization. In contrast, microbial community was highly responsive (low resistance) to inorganic fertilization alone or plus wheat straw, which was associated with lower crop production, nutrient availability, and higher abundance of potential fungal plant pathogens. Our work demonstrates that the response of microbial community to long-term nutrient fertilizations largely regulates plant production in agricultural ecosystems, and suggests that manipulating these microbial phylotypes may offer a sustainable solution to the maintenance of field productivity under long-term nutrient fertilization scenarios.

Dose-dependent effect of compost amendment on soil bacterial community composition and co-occurrence network patterns in soybean agroecosystem

ABSTRACT This study aimed to elucidate the effects of various doses of compost amendment on bacterial community compositions and co-occurrence network patterns across the growing season in black soil, Northeast China. Bacterial richness was unaffected by compost addition in seedling and flowering stage, whereas significantly enhanced by high level of compost addition (45,000 kg ha−1) in mature stage. Non-metric multidimensional scaling analysis revealed distinct bacterial communities in response to compost addition across the growing season. At phylum level, copiotrophic groups of bacteria including Bacteroidetes and Firmicutes gradually increased in relative abundance along with compost rate, while oligotrophic groups (Planctomycetes and Verrucomicrobia) showed opposite tendency. Notably, these enrichment or reduction was most pronounced in seedling stage. Abundant genera including Actinomadura, Aminobacter, Cellvibrio, Devosia, Luteimonas, Microbacterium, Nonomuraea, Promicromonospora were positively and consistently correlated with compost rate, whereas Arthrobacter, Flavisolibacter, Janthinobacterium, Kaistobacter negatively correlated. Network analysis indicated that compost amended soils (40.0, 49.0, and 64.0%) harbored more positive links than control (37.6%). In addition, the soil bacterial network connectivity and connectedness generally increased along with the compost rate, while modularity exhibited opposite trend. Overall, our findings show that compost addition modified the bacterial community compositions and network patterns in soybean agroecosystem in Northeast China.

Higher temporal turnover of soil fungi than bacteria during long-term secondary succession in a semiarid abandoned farmland

Microorganisms play critical roles in soil biogeochemical processes and the establishment of vegetation communities. However, their long-term successional patterns and associations with environmental factors are not well understood, especially in semiarid areas where plant community composition and species diversity change rapidly. We investigated changes in soil (Cambisol) microbial communities across a chronosequence of abandoned farmland comprising six successional stages (0, 11, 35, 60, 100, and 150-years) in the semiarid Loess Plateau of China. We aimed to reveal the long-term patterns and succession rates of microbial communities, and to reveal the driving forces. Bacterial and fungal communities were characterized by sequencing bacterial 16S ribosomal RNA genes and fungal internal transcribed spacers (ITS), respectively. Temporal turnover of microbial succession was investigated using the slope (w value) of linear regression of log-transformed microbial community similarity over time. Succession rate of fungi was approximately three times higher (w = 0.1477, P < 0.0001) than that of bacteria (w = 0.0549, P < 0.0001). Bacterial succession was affected by changes in soil NH4+-N, total N, organic C, water content, bulk density, and pH, whereas fungi were more susceptible to changes in NO3−-N, available phosphorus, and C:N ratio. Bacterial communities transitioned from slow-growing oligotrophic groups (Gemmatimonadetes, Chloroflexi) to fast-growing copiotrophic groups (Alpha- and Betaproteobacteria). Basidiomycota showed the highest temporal turnover (w = 0.2000, P < 0.0001), followed by Armatimonadetes, Firmicutes, Verrucomicrobia, Chloroflexi, and Proteobacteria. These results provide new insights into microbial community dynamics during long-term secondary succession, and enhance our understanding of associations between soil factors and microbes in semiarid ecosystems.

Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river

Anthropogenic activity-mediated nutrient pollution, especially nitrogen enrichment, poses one of the major threats to river ecosystems. However, it remains unclear how and to which extent it affects aquatic microbial communities, especially in heavily polluted rivers. In this study, a significant environmental gradient, particularly nitrogen gradient, was observed along a wastewater receiving river, the North Canal River (NCR). The pollution level was highest, moderate, and lowest in the up-, middle, and down-streams, respectively. The community composition of bacterioplankton transitioned from being Betaproteobacteria-dominated upstream to Gammaproteobacteria-dominated downstream. Copiotrophic groups, such as Polynucleobacter (Betaproteobacteria) and Hydrogenophaga (Betaproteobacteria), were dominant in the upstream. Multiple statistical analyses indicated that total nitrogen (TN) was the most important factor driving the adaptive shifts of community structure. Analyses of co-occurrence networks showed that the complexity of networks was disrupted in the up- and middle streams, while enhanced in the downstream. Our findings here suggested that microbial interactions were reduced in response to the aggravation of nutrient pollution. Similar to these changes, we observed significant dissimilarity of composition of functional groups, with highest abundance of nitrogen metabolism members under the highest level of nitrogen enrichment. Further analyses indicated that most of these functional groups belonged to Betaproteobacteria, suggesting the potential coupling of community composition and function diversity. In summary, adaptive shifts of bacterioplankton community composition, as well as species interactions, occurred in response to nutrient pollution in highly polluted water bodies.

Spatial distribution of microbial community composition along a steep slope plot of the Loess Plateau

Spatial heterogeneity of soil microbes introduces great uncertainty to our understanding of microbe-mediated soil carbon cycling, yet was few studied on sloping lands. Along a steep-slope grassland (35°) on the Chinese Loess Plateau, soils of 0–10 cm were sampled in 2016 at three slope positions (upper, middle and bottom) to determine microbial community composition (by Illumina Hiseq sequencing) and function (enzymes involved in carbon cycling, the in situ soil respiration and temperature sensitivity). The bacterial alpha-diversity were greater at middle- and bottom- than at upper slope position, while fungal alpha-diversity varied little across slope positions. The bacterial phylum Proteobacteria was 9.7% and 19.4% lower but Acidobacteria was 36.5% and 41.3% greater at bottom- than at upper- and middle- slope positions. The fungal community transitioned from being Basidiomycota-dominant (relative abundance of 46.8%) at upper slope position to Zygomycota-dominant (relative abundance of 36.5%) at bottom slope position. The β-d-glucosidase activity generally declined down the slope while β-d-xylosidase and cellobiohydrolase activities hiked at middle slope position. All the enzyme activities were suppressed at bottom slope position. Soil respiration increased by 49.1% (P < 0.05) while temperature sensitivity decreased by 13.2% (P < 0.05) down the slope. Both bacterial richness (OTU) and diversity (Shannon diversity index) positively correlated with soil respiration. The copiotrophic groups (Acidobacteria and Zygomycota) negatively and oligotrophic groups (Proteobacteria and Basidiomycota) positively correlated with temperature sensitivity of soil respiration. Our findings revealed divergent responses of soil bacterial and fungal communities along the slope and highlighted the importance of microbial information in predicting the spatial variability of soil respiration in hillslope ecosystems.

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau

Thinning can effectively improve forest production and maintain ecological stability. However, the changes in soil microbial community compositions after thinning are still not well understood. In this study, we investigated the changes in the soil microbial community of mature Chinese pine (Pinus tabuliformis) plantations in the Loess Plateau after 11years of four different thinning intensity treatments. Furthermore, the responses of the soil microbial community to changes in understory plants and soil properties were analyzed. The ratios of wood removal investigated were 0 (CK), 15% (LIT), 30% (MIT) and 45% (HIT). Compared with the CK, thinning significantly increased the Shannon index, species richness, coverage and biomass of the understory plants, and these values were highest for the HIT. The soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO3−-N) and available phosphorus (AP) concentrations increased with increasing thinning intensity. Thinning intensity did not significantly affect soil microbial community diversity indices. With respect to the dominant bacterial groups, the relative abundance of Proteobacteria was much higher in the HIT, while that of Acidobacteria was much higher in the LIT and CK. For the dominant fungal groups, the relative abundance of Basidiomycota was lowest in the HIT, while that of Ascomycota was highest in the same treatment. Redundancy analysis (RDA) showed that SOC, TN, and AP significantly correlated with soil bacterial communities and that SOC, TN, TP, AP and NO3−-N significantly correlated with soil fungal communities. The understory vegetation influenced soil fungal communities rather than soil bacterial communities. These findings suggest that the aboveground vegetation diversity and soil nutrients were improved with the increased thinning intensity after 11years. The copiotrophic groups (e.g. Proteobacteria) and oligotrophic groups (e.g. Acidobacteria) differed significantly among the four thinning treatments, indicating a dependence of the soil microbial community composition on soil nutrients.