Arbuscular mycorrhiza and plant chromium tolerance Abstract Arbuscular mycorrhizal (AM) fungi are ubiquitous soil fungi that form symbiotic associations with most terrestrial plants. The growth and functions of AM fungi depend on carbohydrates supplied by the plants, in return, the fungi assist the plants to acquire mineral nutrients (e.g., phosphorus) from soil. The AM symbiosis also improves plant survival in various unfavorable environments, such as metal (loid) contaminated soil. It has been well demonstrated that AM symbiosis improved plant adaptation to Cr contamination, which would have a great potential in phytoremediation and ecological restoration of Cr contaminated soils. In this paper, we have reviewed the role of AM fungi in alleviation of Cr phytotoxicity and associated factors influencing plant Cr tolerance. AM symbiosis improves plant Cr tolerance through its direct roles in Cr stabilization and transformation and indirect roles via AM symbiosis mediated nutrient acquisition and physiological regulation. Future research on physiological and molecular mechanisms underlying Cr behavior and detoxification in AM symbiosis, as well as potential use of AM fungi in ecological restoration and agriculture production in Cr contaminated soils were also proposed.

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam Abstract Soil redox is a critical environmental factor shaping the microbial community structure and ultimately alters the nutrient cycling. However, the response of soil microbial community structure to prolonged or repeated redox fluctuations is not yet clear. To study the dynamic effects of prolonged redox disturbances to the soil microbial community structure, soil samples experiencing 8, 5 and 0 alternating oxic-anoxic cycles within approximately 6 months each year were collected and the microbial community structure were evaluated using phospholipid fatty acid analysis (PLFA) profiles. Prolonged redox disturbances had significant effects on soil physiochemical properties and soil microbial community structure. The relative abundance of straight chain saturated PLFAs, cyclopropyl, and terminal- and mid-branched chain saturated PLFAs increased due to prolonged redox disturbances, but there was a consistent decrease in linear monounsaturated PLFAs and polyunsaturated PLFAs in the fluctuating zone. Prolonged redox disturbances had a negative impact on the total PLFA content (a proxy for biomass). Both the fluctuating zone (8-cycle and 5-cycle plots) and the never flooded zone (0-cycle plots) were dominated by Gram-positive bacteria and a low content of fungi, actinomycetes and protozoa. The fungi and protozoa abundance decreased significantly with an increase in the occurrence of alternating flooding-dry events, suggesting that the prolonged redox disturbance leads to high stress on the fungi and protozoa populations. Moreover, total organic matter (TOC) and C:N ratio, environmental factors that can be influenced by recurring redox fluctuations, also influenced the microbial community structure.

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil Abstract To determine the effects of different kinds of nitrogen fertilizer, especially high-efficiency slow-release fertilizers, on soil pH, nitrogen (N) and microbial community structures in an acidic celery soil, four treatments (CK, no N fertilizer; NR, urea; PE, calcium cyanamide fertilizer; and SK, controlled-release N fertilizer) were applied, and soil pH, total soil N, inorganic N, and soil microbial biomass C were analyzed. Phospholipid fatty acids (PLFAs) were extracted and detected using the MIDI Sherlock microbial identification system. The PE treatment significantly improved soil pH, from 4.80 to >6.00, during the whole growth period of the celery, and resulted in the highest celery yield among the four treatments. After 14 d application of calcium cyanamide, the soil nitrate content significantly decreased, but the ammonium content significantly increased. The PE treatment also significantly increased soil microbial biomass C during the whole celery growth period. Canonical variate analysis of the PLFA data indicated that the soil microbial community structure in the CK treatment was significantly different from those in the N applied treatments after 49 d fertilization. However, there was a significant difference (P<0.05) in soil microbial community structure between the PE treatment and the other three treatments at the end of the experiment. Calcium cyanamide is a good choice for farmers to use on acidic celery land because it supplies sufficient N, and increases soil pH, microbial biomass and the yield of celery.

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils Abstract To evaluate the effect of organic amendments on soil nematode community composition and diversity within aggregate fractions, a study was initiated in agricultural soils with four-year organic amendments. Soil samples were collected from the plow layer (0–20 cm) under three cornfield management scenarios: 1) conventional cropping (CK, corn straw removal and no organic manure application); 2) straw retention (SR, incorporation of chopped corn stalk); and 3) manure application (MA, chicken manure input). The soil samples were fractionated into four aggregate sizes, i.e., >2 mm (large macroaggregates), 1–2 mm (macroaggregates), 0.25–1 mm (small macroaggregates), and <0.25 mm (microaggregates, silt and clay fractions). The composition and diversity of soil nematode communities were determined within each aggregate fraction. The results showed that both SR and MA treatments significantly increased the percentage of macroaggregates (>1 mm) and only MA treatment strongly increased the mean weight diameter compared to the CK (P<0.05). The abundance of total nematodes and four trophic groups were affected significantly by the aggregate fractions and their higher abundance occurred in the larger aggregates. The effects of aggregate size on most nematode genera were significant. Bacterivores in the small macroaggregates and microaggregates, and fungivores in the large macroaggregates were significantly different among treatments. The percentage of bacterivores increased after the application of organic materials, while that of fungivores decreased. It can be concluded that organic management significantly affects soil aggregation and soil characteristics within aggregates, and the aggregate size subsequently influences the distribution of nematode communities.

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization Abstract Archaeal and bacterial ammonia-oxidizers drive the first step of nitrification, ammonia oxidation. Despite their importance, the relative contribution of soil factors influencing the abundance, diversity and community composition of ammonia oxidizing archaea (AOA) and bacteria (AOB) are seldom compared. In this study, the AOA and AOB communities in soils from a long-term fertilization experiment (which formed gradients of pH and nutrients) were measured using 454 pyrosequencing of the amoA gene. Results showed that both AOA and AOB communities were influenced by fertilization practice. Changes of AOA abundance, diversity and community structure were closely correlated with a single factor, soil pH, and the abundance and diversity of AOA were lower under the acidified treatments. By contrast, AOB abundance was higher in the acidified soil than in the control soil while AOB diversity was little impacted by soil acidification, and both the abundance and diversity of AOB were most highly correlated with soil carbon and available phosphorus. These results indicated that AOB diversity seemed more resistant to soil acidification than that of AOA, and also suggested that AOB have greater ecophysiological diversity and broader range of habitats than AOA in this lime concretion black soil, and the potential contribution of AOB to ammonia oxidation in acid environments should not be overlooked.

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils Abstract An experiment was conducted to improve rhizoremediation for decabromodiphenyl ether (BDE-209) contaminated soil from typical E-waste dismantling areas. Plants of ryegrass (Lolium perenne L.) and rice (Oryza sativa L.) were cultivated in aged-contaminated (initial concentration of 346.3 μg BDE-209$kg−1) and freshly-spiked (initial concentration of 3127 μg BDE-209$kg−1) soils, coupling with the agricultural modification strategies of compost addition and/or arbuscular mycorrhizal fungi (AMF) infection, respectively. 60 days’ growth of ryegrass significantly facilitated the dissipation of BDE-209, with the most effective in its rhizosphere in treatment inoculated with AMF; the BDE-209 dissipation rates achieved 51.9% and 22.8% in rhizosphere, and 43.5% and 19.8% in non-rhizosphere, for aged-contaminated and freshly-spiked soils, respectively. 120 days’ growth of rice with simultaneous inoculation of AMF and addition of compost was the most effective in facilitating BDE-209 dissipation in aged-contaminated soil, with the removal rates of 53.3% and 48.1% in rhizosphere and non-rhizosphere soils respectively; while for freshly-spiked soils, the most effective removal was achieved by compost addition only, with the BDE-209 dissipation rates of 27.9% and 26.6% in rhizosphere and non-rhizosphere soils, respectively. High throughput sequencing analysis of rhizosphere soil DNA showed that responses in microbial communities and their structure differed with plant species, soil pollution dose, AMF inoculation and/or compost addition. Actinomycetales, Xanthomonadales, Burkholderiales, Sphingomonadales, Clostridiales, Cytophagales, Gemmatimonadales and Saprospirales were the sensitive responders and even possibly potential functional microbial groups during the facilitated removal of BDE-209 in soils. This study illustrates an effective rhizoremediation pattern for removal of BDE-209 in pollution soils, through successive cultivation of rice and followed by ryegrass, with rice growth coupled with AMF inoculation and compost addition, while ryegrass growth coupled with AMF inoculation only.

Community assemblage of free-living diazotrophs along the elevational gradient of Mount Gongga Abstract Mountain systems are unique for studying the responses of species distribution and diversity to environmental changes along elevational gradients. It is well known that free-living diazotrophic microorganisms are important to nitrogen cycling in mountain systems. However, the elevational patterns of free-living diazotrophs and the underlying ecological processes in controlling their turnover along broader gradients are less well documented. Here, we investigated the pattern of diazotrophic diversity along the elevational gradient (1800 m-4100 m) in Mount Gongga of China. The results showed that the α-diversity of diazotrophs did not change with the elevation from 1800 m to 2800 m, but decreased at elevations above 3000 m. Such diversity pattern was driven mainly by soil total carbon, nitrogen, and plant richness. Various diazotrophic taxa showed differential abundance-elevation relationships. Ecological processes determining diazotrophic community assemblage shift along the elevations. Deterministic processes were relatively stronger at both low and high elevations, whereas stochastic processes were stronger at the middle elevation. This study also suggested a strong relationship among aboveground plants and diazotrophs, highlighting their potential interactions, even for free-living diazotrophs.

Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization Abstract Soil is inhabited by a myriad of microorganisms, many of which can form supracellular structures, called biofilms, comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival. Biofilms enable intensive inter- and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins. Here, we first discuss organization, dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome. Social interactions among bacteria, such as cooperation and competition, are discussed. We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms. Microfluidic platforms, which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with high-throughput screening and novel measurements, are also highlighted. This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.

Exploring soil microbial communities: Opportunities for soil ecology research

A biogeographic map of soil bacterial communities in wheats field of the North China Plain Abstract The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production. Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services, thus providing valuable insights to improve food production. The North China Plain (NCP) is one of the world’s key agricultural regions, supplying more than 50% of the cereal consumed in Asia. However, it is unknown whether soil microbial diversity is predictable across the NCP. Using the MiSeq Illumina platform, we examined bacterial community variation in relation to spatial and environmental factors from 243 soils in wheat-maize double cropping rotation fields across the NCP, which cover nearly 0.3 million km2. Based on observed bacterial communities and their relationships with environmental factors, we generated a map of bacterial communities across the NCP. The highest bacterial diversity was found in the middle part of the NCP, with most of the variation in diversity attributable to differences in the community similarity of Actinobacteria and Alphaproteobacteria. These findings provide important baseline information for analyzing the relationships between microbial community, soil functionality and crop yields.