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Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26–8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18–20.68 mg kg −1 ) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes.

Background Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria , one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with 13 C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition. Results While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and 13 C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility. Conclusions This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling. 3uWhKDWFjqsFeP9DMWUatJ Video abstract

Background Soil microbial community and diversity are key in sustaining soil ecosystem health. In recent years, the health of soil ecosystems has been severely threatened by the large input of synthetic fertilizers and the continuous monocropping in greenhouse-based intensive production systems. As a result, the N utilization efficiency has significantly decreased, which has had adverse impacts on soil, water, and the atmosphere. Additionally, soil-borne plant diseases are more frequent in greenhouse-based intensive vegetable systems. Shifts in the microbial community structure and diversity largely account for these continuous cropping problems in vegetable agricultural soils. Scope In this review, soil microbial deterioration, including microbial activities, C source utilization patterns, nitrification, microbial community composition, and arbuscular mycorrhizal fungi are summarized. Soil microbial deterioration is due to the excessive use of fertilizers, which have caused soil secondary salinization and acidification, pollutants brought on by intensive vegetable agriculture, and principally continuous cropping of same or similar vegetable species. Conclusions Therefore, measures must be taken to restore soil microbial communities, including rational fertilization, rotation or intercropping, cultivation of catch or cover crops, and reductive soil disinfestation. Rational fertilization, such as the reduction in chemical N fertilization levels, substitution of chemical fertilizer by organic manure, and the use of bio-fertilizer and bio-organic fertilizer, is of decisive importance. This review provides a better understanding of ecosystem health in vegetable agricultural soils and recommends effective measures to improve the health of these ecosystems.

The effects of mineral fertilizer (NPK) and organic manure on phospholipid fatty acid profiles and microbial functional diversity were investigated in a long-term (21-year) fertilizer experiment. The experiment included nine treatments: organic manure (OM), organic manure plus fertilizer NPK (OM + NPK), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer N (N), fertilizer P (P), fertilizer K (K), and the control (CK, without fertilization). The original soil was extremely eroded, characterized by low pH and deficiencies of nutrients, particularly N and P. The application of OM and OM + NPK greatly increased crop yields, soil pH, organic C, total N, P and K, available N, P and K content. Crop yields, soil pH, organic C, total N and available N were also clearly increased by the application of mineral NPK fertilizer. The amounts of total PLFAs, bacterial, Gram-negative and actinobacterial PLFAs were highest in the OM + NPK treatment, followed by the OM treatment, whilst least in the N treatment. The amounts of Gram-positive and anaerobic PLFAs were highest in the OM treatment whilst least in the P treatment and the control, respectively. The amounts of aerobic and fungal PLFAs were highest in the NPK treatment whilst least in the N and P treatment, respectively. The average well color development (AWCD) was significantly increased by the application of OM and OM + NPK, and the functional diversity indices including Shannon index (H ′ ), Simpson index (D) and McIntosh index (U) were also significantly increased by the application of OM and OM + NPK. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from nine fertilizer treatments. The PLFA profiles from OM, OM + NPK, NP and NPK were significantly different from that of CK, N, P, K and NK, and C source utilization patterns from OM and OM + NPK were clearly different from organic manure deficient treatments (CK, N, P, K, NP, NK 6 and NPK). Stepwise multiple regression analysis showed that total N, available P and soil pH significantly affected PLFA profiles and microbial functional diversity. Our results could provide a better understanding of the importance of organic manure plus balanced fertilization with N, P and K in promoting the soil microbial biomass, activity and diversity and thus enhancing crop growth and production.

The diversity of eukaryotic macroorganisms such as animals and plants usually declines with increasing elevation and latitude. By contrast, the community structure of prokaryotes such as soil bacteria does not generally correlate with elevation or latitude, suggesting that differences in fundamental cell biology and/or body size strongly influence diversity patterns. To distinguish the influences of these two factors, soil eukaryotic microorganism community structure was investigated in six representative vegetation sites along an elevational gradient from forest to alpine tundra on Changbai Mountain in Northeast China, and compared with our previous determination of soil bacterial community structure along the same gradient. Using bar-coded pyrosequencing, we found strong site differences in eukaryotic microbial community composition. However, diversity of the total eukaryotic microorganism community (or just the fungi or protists alone) did not correlate with elevation. Instead, the patterns of diversity and composition in the total eukaryotic microbial community (and in the protist community alone) were closely correlated with soil pH, suggesting that just as for bacteria, acidity is a particularly important determinant of eukaryotic microbial distributions. By contrast, as expected, plant diversity at the same sites declined along our elevational gradient. These results together suggest that elevational diversity patterns exhibited by eukaryotic microorganisms are fundamentally different from those of plants.

Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity.

Silver nanoparticles (AgNPs) are considered to be emerging contaminant for plant-soil systems. AM arbuscular mycorrhizal (AM) fungi can alleviate the negative effects of a variety of pollutants on their hosts, but its potential roles in influencing the toxicity of AgNPs and the underlying mechanisms are still an open question. This study investigated the responses of maize ( Zea mays L.) inoculated with or without AM fungi and soil microorganisms to different concentrations of AgNPs (0, 0.025, 0.25, and 2.5 mg kg −1 ). The inoculation of AM fungi helps to alleviate the AgNP-induced phytotoxicity. Compared to the non-AM fungal inoculated treatments, AM fungal inoculation significantly increased the mycorrhizal colonization, biomass and phosphorus (P) acquisitions of maize, with an upregulation of P transporter gene expression under AgNP treatments. AM fungal inoculation decreased Ag content in plant shoots and roots, downregulated expression levels of genes involved in Ag transport and gene encoding a metallothionein involved in metal homeostasis. The beneficial role of AM fungi extended to soil microbes. Compared to the non-AM fungal inoculated treatments, AM fungal inoculation decreased the toxicity of AgNPs to soil microbial activities and bacterial abundance. AM fungal inoculation increased the bacterial diversity and induced changes in the soil bacterial community composition. Altogether, the present study revealed that AM fungal symbiosis can play beneficial roles in mediating the negative effects exposed by AgNPs on plants probably through changing the expressions of potential Ag transporters and cooperating with soil bacterial community.

Straw, mainly dry stalks of crops, is an agricultural byproduct. Its incorporation to soils via microbial redistribution is an environment-friendly way to increase fertility. Fertilization influences soil microorganisms and straw degradation. However, our up to date knowledge on the responses of the straw decomposers to fertilization remains elusive. To this end, inoculated with paddy soils with 26-year applications of chemical fertilizers, organic amendments or controls without fertilization, microcosms were anoxically incubated with 13 C-labelled rice straw amendment. DNA-based stable isotope probing and molecular ecological network analysis were conducted to unravel how straw degrading bacterial species shift in responses to fertilizations, as well as evaluate what their roles/links in the microbiome are. It was found that only a small percentage of the community ecotypes was participating into straw degradation under both fertilizations. Fertilization, especially with organic amendments decreased the predominance of Firmicutes - and Acidobacteria -like straw decomposers but increased those of the copiotrophs, such as β- Proteobacteria and Bacteroidetes due to increased soil fertility. For the same reason, fertilization shifted the hub species towards those of high degrading potential and created a more stable and efficient microbial consortium. These findings indicate that fertilization shapes a well-organized community of decomposers for accelerated straw degradation.

PurposeContinuous cropping of tomato (Solanum lycopersicum Mill.) causes soil degradation, accumulating Ralstonia solanacearum that induce Ralstonia wilt notably in plastic shed soils. Arbuscular mycorrhizal (AM) fungi play a crucial role in protecting hosts against such soil-borne pathogens, but comprehensive understanding of the soil–plant defense systems upon mycorrhization is not clear yet, especially at the later period of fruit production. The aim of this study was to investigate the underlining mechanisms in both soil and plant.Materials and methodsA 10-week greenhouse pot experiment with four treatments, including control and inoculation with Funneliformis caledonium (Fc), R. solanacearum (Rs), and both strains (Rs + Fc), was carried out on a sterilized soil. Pots with two tomato plants each were randomly arranged with six replicates per treatment. The wilt severity; the tissue biomass and nutrient content; the root mycorrhizal colonization and total phenolic compounds; the leaf peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia lyase (PAL) activities; and soil AM fungi and R. solanacearum abundances, soil pH, organic C and nutrient concentrations, and phosphatase activity were all tested. Both redundancy analysis (RDA) and structural equation modeling (SEM) were performed to illustrate plant overall performance among treatments and to elucidate the major influencing pathways of AM fungi.Results and discussionThe additional inoculation with F. caledonium resulted in significant decreases of soil R. solanacearum abundance and Olsen-P concentration, as well as increases of soil pH, organic C concentration, and phosphatase activity, as compared to the soil only inoculated with R. solanacearum. Mycorrhizal inoculation also increased root total phenolic compound content, and leaf POD and PPO activities, but reduced shoot/root K ratio in plants under the attack of R. solanacearum, thereby alleviating Ralstonia wilt severity by 65.7% and yield loss by 46.5%. The RDA and SEM results revealed significant variation in plant overall performance among treatments, and the contribution of AM fungi in suppressing tomato Ralstonia wilt and yield damage particularly via ameliorating soil quality and alleviating plant metabolic pressure.ConclusionsThis study verified the bio-protection of AM fungi in both soil and plant systems against tomato Ralstonia wilt. Mycorrhization shifted the soil environment and suppressed soil R. solanacearum population, and also modulated plant nutrient translocation, increased phenolic compounds synthetization, and activated defense enzymes. Through establishing the integrated defense systems in both rhizosphere and plant, AM fungi alleviated the severity of Ralstonia disease and ameliorated yield damage in tomato.

The phyllosphere, the aerial parts of terrestrial plants, represents the largest biological interface on Earth. This habitat is colonized by diverse microorganisms that affect plant health and growth. However, the community structure of these phyllosphere microorganisms and their responses to environmental changes, such as rising atmospheric CO₂, are poorly understood. Using a massive parallel pyrosequencing technique, we investigated the feedback of a phyllosphere bacterial community in rice to elevated CO₂ (eCO₂) at the tillering, filling, and maturity stages under nitrogen fertilization with low (LN) and high application rates (HN). The results revealed 9,406 distinct operational taxonomic units that could be classified into 8 phyla, 13 classes, 26 orders, 59 families, and 120 genera. The family Enterobacteriaceae within Gammaproteobacteria was the most dominant phylotype during the rice growing season, accounting for 61.0–97.2 % of the total microbial communities. A statistical analysis indicated that the shift in structure and composition of phyllosphere bacterial communities was largely dependent on the rice growing stage. eCO₂ showed a distinct effect on the structure of bacterial communities at different growth stages, and the most evident response of the community structure to eCO₂ was observed at the filling stage. eCO₂ significantly increased the relative abundance of the most dominant phylotype (Enterobacteriaceae) from 88.6 % at aCO₂ (ambient CO₂) to 97.2 % at eCO₂ under LN fertilization at the filling stage, while it significantly decreased the total relative abundance of other phylotypes from 7.48 to 1.35 %. Similarly, higher value for the relative abundance of the most dominant family (Enterobacteriaceae) and lower value for the total relative abundance of other families were observed under eCO₂ condition at other growth stages and under different N fertilizations, but the difference was not statistically significant. No consistent response pattern was observed along growth stages that could be attributed to N treatments. These results provide useful insights into our understanding of the response of a phyllosphere bacterial community to eCO₂ with regards to the diversity, composition, and structure during rice growing seasons.