Spatial structuring of soil microbial communities in commercial apple orchards

Summary Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient‐poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2 years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate‐induced respiration rate and a 5‐fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P‐fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro‐organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram‐positive : Gram‐negative ratio. The Fungi : Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

Effects of tree species transition on soil microbial biomass and community structure in subtropical China

Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates.

To gain better knowledge of the effects of residual chlorothalonil on soil characteristics and soil microbial communities, we evaluated the dissipation of chlorothalonil and the effects of different chlorothalonil concentrations on soil respiration, enzyme activities, and microbial community structure in yellow–brown loam soils. Bacterial and fungal soil communities were examined using traditional plate counting and polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) methods. Soil properties and the results of DGGE band analysis were both used to estimate the status of the soil microbial ecosystem. The results show that residual chlorothalonil has considerable effects on soil respiration, enzymatic activities, and microbial community structure. In particular, soil respiration and phosphatase activities were increased, while saccharase activity, microbial biomass, and microbial community diversity were decreased by increasing levels of chlorothalonil treatment. Correlation analyses revealed that the application of chlorothalonil was significantly correlated with the change of the soil respiration, urease activity, sucrase activity, soil culturable bacteria, and culturable fungi biomass. We conclude that residual chlorothalonil is directly related to soil respiration, enzyme activities, and microbial community structure.

Biochar effects on soil microbial abundance and community structure are keys for understanding the biogeochemical cycling of nutrients and organic matter turnover, but are poorly understood, in particular in tropical areas. We conducted a greenhouse experiment in which we added biochars produced from four different feedstocks [sewage sludge (B1), deinking sewage sludge (B2), Miscanthus (B3) and pine wood (B4)] at a rate of 3% (w/w) to two tropical soils (an Acrisol and a Ferralsol) planted with proso millet (Panicum milliaceum L.). The interactive effect of the addition of earthworms was also addressed. For this purpose we utilized soil samples from pots with or without the earthworm Pontoscolex corethrurus, which is a ubiquitous earthworm in tropical soils. Phospholipid fatty acid (PLFA) measurements showed that biochar type, soil type and the presence of earthworms significantly affected soil microbial community size and structure. In general, biochar addition affected fungal but not bacterial populations. Overall, biochars rich in ash (B1 and B2) resulted in a marked increase in the fungi to bacteria ratio, while this ratio was unaltered after addition of biochars with a high fixed carbon content (B3 and B4). Our study remarked the contrasting effect that both, biochar prepared from different materials and macrofauna, can have on soil microbial community. Such changes might end up with ecosystem-level effects.

Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9–17% in predicting the structure of soil microbial communities with up to 69–78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.

Fertilizer applications have important effects on soil microbial abundance and community structure. In this study, total soil microbial DNA and RNA were directly extracted from paddy soils of N0 (control treatment, no nitrogen fertilizer), NPK (balanced fertilization), NPK+LS (balanced fertilization with additional 3.0 t·hm-2 rice straw incorporation) and NPK+HS (balanced fertilization with additional 6.0 t·hm-2 rice straw incorporation) treatments in a long-term fertilization experiment of double rice cropping system in Changsha County, Hunan Province. Soil bacteria community structures were evaluated by analyzing the 16S rRNA gene fragments at DNA and cDNA levels with Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR techniques. Balancing fertilization with chemical fertilizers and rice straw incorporation significantly changed the composition of bulk (DNA-based) and potentially active (mRNA-based) soil bacterial community as shown in T-RFLP profiles, and also reduced the bulk soil microbial diversity, but not the potentially active ones, as compared with the control treatment. The DNA-based abundance of 16S rRNA gene was on average 377 times as many as the m-RNA based population size. Compared to N0,balanced fertilization with rice straw incorporation (NPK+LS and NPK+HS) increased the bulk and active copy numbers of 16S rRNA gene, but not for balanced fertilization (NPK). The abundance and microbial community structure were not significantly different between the NPK+LS and NPK+HS treatments. Redundancy analysis (RDA) showed that soil ammonium was the key environmental factor determining the bulk and active soil microbial community structure among the treatments. In conclusion, the effect of fertilization on soil microbial abundance and community structure could be indicated at both DNA and cDNA levels; the cDNA information could better reflect the adaptability of bacterial community to the environmental stress.

The strong seasonality of soil microbial community structure in declining Mediterranean pine forests depends more on soil conditions than on tree vitality

This research aimed to reveal the response characteristics of soil microbial community structure to different degrees of tourism disturbance. To explore the soil microbial community structure’s response mechanism, we set up continuous plots with different interference intensities: high disturbance, middle disturbance, and the control area. We collected 0–10 cm topsoil in all plots and used Illumina MiSeq high-throughput sequencing method to obtain and analyze the response characteristics of soil microbial community composition and structure under different tourism disturbances. These results were then combined with alpha diversity and environmental factors to explore the microbial response mechanism. In the tested soil, Acidobacteria, Chlorocurve, and Proteobacteria were the main bacterial phyla, while Basidiomycota and Ascomycota were the main fungal phyla. Based on the phylum, the relative abundance of the microbial community between the interference groups was compared using a significance test, with significant differences found between the interference groups in the phyla Chloroflexus, GAL15, Rokubacteria, and Blastomonas (p < 0.05). The relative abundance of the dominant phyla in the fungal community was significantly different among the groups (p < 0.05). A principal component analysis of the soil microbial community structure suggested that the soil microbial community structure was significantly different for different interference levels.

Application of manure from cattle administered antibiotics has sustained multi-year impacts on soil resistome and microbial community structure

Does plant diversity drive soil microbial diversity in temperate, upland grasslands? Plants influence microbial activity around their roots by release of carbon and pot studies have shown an impact of different grass species on soil microbial community structure. Therefore it is tempting to answer yes. However, evidence from field studies is more complex. This evidence is reviewed at three different scales. First, studies from the plant community scale are considered that have compared soil microbial community structure in pastures of different vegetation composition, as a consequence of pasture improvement. These show fungi dominating the biomass in unimproved pastures and bacteria when lime and fertilizers have been applied. Secondly, evidence for interactions between individual grass species and soil microbes is discussed at the level of the rhizosphere, by considering both pot experiments and field studies. These have produced contrasting and inconclusive results, often due to spatial heterogeneity of soil properties and microbial communities. In particular, increased soil pH and fertility in urine patches and other nutrient cycling processes interact to increase the spatially complexity of soil microbial communities. Finally three studies which have measured microbial community structure in the rhizoplane are considered. These show that bacterial diversity is not directly related to plant diversity, although fungal diversity is. In addition, the soil fungal community has been demonstrated to have an effect upon the composition of the bacterial community. We suggest that while current vegetation influences fungal communities (particularly mycorrhizae) and litter inputs fungal saprotrophs, bacterial community structure is influenced more by the quality or composition of soil organic matter, thereby reflecting carbon inputs to the soil over decades.

A glasshouse experiment was undertaken to provide baseline data on the variation between conventional maize (Zea mays L.) varieties and genetically modified maize plants expressing the insecticidal Bacillus thuringiensis protein (Bt, Cry1Ab). The objective was to determine whether the variation in soil parameters under a range of conventional maize cultivars exceeded the differences between Bt and non-Bt maize cultivars. Variations in plant growth parameters (shoot and root biomass, percentage carbon, percentage nitrogen), Bt protein concentration in shoots, roots and soil, soil nematode abundance and soil microbial community structure were determined. Eight paired varieties (i.e. varieties genetically modified to express Bt protein and their near-isogenic control varieties) were investigated, together with a Bt variety for which no near-isogenic control was available (NX3622, a combined transformant expressing both Bt and herbicide tolerance) and a conventional barley (Hordeum vulgare L.) variety which was included as a positive control. The only plant parameter which showed a difference between Bt varieties and near-isogenic counterparts was the shoot carbon to nitrogen ratio; this was observed for only two of the eight varieties, and so was not attributable to the Bt trait. There were no detectable differences in the concentration of Bt protein in plant or soil with any of the Bt-expressing varieties. There were significant differences in the abundance of soil nematodes, but this was not related to the Bt trait. Differences in previously published soil nematode studies under Bt maize were smaller than these varietal effects. Soil microbial community structure, as determined by phospholipid fatty acid (PLFA) analysis, was strongly affected by plant growth stage but not by the Bt trait. The experimental addition of purified Cry1Ab protein to soil confirmed that, at ecologically relevant concentrations, there were no measurable effects on microbial community structure.

The effects of four Picea asperata plantations with different ages (50-, 38-, 27- and 20-year-old), in subalpine of western Sichuan, on the characteristics of soil microbial diversity and microbial community structure were studied by the method of phospholipid fatty acid (PLFA) profiles. The results showed that, with the increase of age, the contents of soil organic carbon and total nitrogen gradually improved, while Shannon's diversity index and Pielou's evenness index of soil microorganisms increased at first and then decreased. The amounts of microbial total PLFAs, bacterial PLFAs, fungal PLFAs, actinobacterial PLFAs, and arbuscular mycorrhizal fungal (AMF) PLFAs in soils consistently increased with increasing age. The principal component analysis (PCA) indicated that the soil microbial communities in different plantations were structurally distinct from each other. The first principal component (PC1) and the second principal component (PC2) together accounted for 66.8% of total variation of the soil microbial community structure. The redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil organic carbon, total nitrogen, total potassium, and fine root mass were the key determinants influencing the microbial community structure. Our study suggested that, with the extension of artificialafforestation time, the soil fertility and microbial biomass were enhanced, and the restoration processes of forest ecosystem were stable.

Timber harvesting alters soil carbon mineralization and microbial community structure in coniferous forests