Diversity Of Soil Microbial Communities Research Articles

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types.

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

Influence of different phytoremediation on soil microbial diversity and community composition in saline-alkaline land

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land. HIGHLIGHTS The effects of different phytoremediation on microbial diversity and community structure were different. Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil. All plants increased the activity of nitrite reductase and decreased the activity of urease.

Effects of conservation tillage on soil microbial community and the function of soil carbon cycling

Agricultural tillage practices significantly affect the structure and function of soil micro-bial community, as well as its control over soil carbon cycling. Conservation tillage practice based on no-tillage and crop straw returning is an important measure to improve soil carbon sequestration and fertility, in which soil microorganisms play a key role. Although many previous studies focus on the structure and function of microbial communities under conservation tillage, our overall understanding of soil microbial responses at community level upon conservation tillage is still lacking, due to the complexity of the soil, environmental factors and the different selections of microbial research methods. Furthermore, previous studies paid more attention to the role of soil microorganisms as decomposers and the contribution of plant-derived carbon to the formation of soil carbon pool, but ignored the contribution of microbial-derived carbon to the formation and stability of soil carbon pool. We summarized the paradigm shift in soil organic matter formation and stability theories, reviewed the research methods of soil microbial community, focused on the effects of conservation tillage on soil microbial biomass, community diversity and composition, carbon metabolism, as well as microbial-derived carbon storage, and proposed suggestions for future study, aiming to provide support for future studies regarding microbial responses and its control over soil carbon dynamics in agroecosystem.

Case study on a coniferous plantation site about inter-annual shifts in microbial communities under short-term detritus input manipulations

Soil microorganisms are key regulators of soil carbon (C) and nutrients cycles in terrestrial ecosystems. However, it remains uncertain how the inter-annual variation in soil microbial community corresponds well with resource availability in the changing environment. Here, we investigated soil microbial community structure and abundance, as well as the associated environmental variables from 2015 to 2017 under different plant detritus input manipulation treatments in a coniferous (Platycladus orientalis (Linn.) Franco) plantation forest ecosystem in subtropical China. Our results showed that the inter-annual variation in soil microbial community was more visible than that caused by detritus input manipulations, owing to the temporal alterations in microclimates and substrate availability. Both aboveground litter removal and root exclusion had more negative effects on the bacterial PLFAs than fungi except half a year after detritus input manipulations. While, soil microbial abundance increased only after three years of litter addition compared to control. Litter removal, especially the no input treatment significantly increased the fungi to bacteria (F:B) and Gram-positive to Gram-negative bacteria (GP:GN) ratios after one and two years of detritus input manipulations. Whereas, the litter addition treatment had minor effects on these parameters. A clear discrimination of microbial community structure among the different detritus input manipulations appeared after two and three years. Both the F:B and GP:GN ratios were positively related to the carbon to nitrogen (C:N) ratio, recalcitrance index of carbon (RIC) and nitrogen (RIN). Overall, our results reveal that the inter-annual variations in soil microbial community are clearly differentiated by the environmental variables and substrate availability that occur in different years and detritus input manipulations. Our results also suggest that due to the vital role of microorganisms in biogeochemical cycling, shifts in the microbial community structure with altered plant detritus input could profoundly affect ecosystem processes in the long run.

Effect of round-shaped silver nanoparticles on the genetic and functional diversity of soil microbial community in soil and “soil-plant” systems

Silver and silver nanoparticles (AgNPs) are extensively used as antimicrobial agents in various products and consequently enter the soil ecosystem, in which they accumulate and can have adverse effects on above and belowground organisms. Since the composition of the soil microbiome could have a significant impact on soil fertility, we focused, in this study, on the effect of AgNPs on soil microbial communities. We evaluated the biomass, plant growth-promoting activities, and microbial genetic (taxonomical) and functional diversity in the soil and the “soil-plant” system using chemical, microbiological, and molecular biological methods, especially qPCR, RFLP, and REP-PCR. By compiling the results of the applied assays, we were able to correlate the changes in genetic diversity with the changes in functional diversity and their impact on the composition of soil organic matter. The effect of AgNPs was predominantly dose-dependent, whereas the concentration 100 mg kgdw−1 had the highest effect on all followed parameters. From the taxonomical point of view, AgNPs had the most significant impact on the relative abundance of Bacteroidetes, which increased in a dose-dependent manner, and Firmicutes, which decreased in a dose-dependent manner, and they caused the predominance of Ascomycota among Fungi. These changes in taxonomic diversity result in a significant decrease in the functional diversity of the microbial communities. Especially for the concentration 100 mg kgdw−1, we detected a significant decrease in the ability of the microbial community to utilize simple carbon substrates, determined by Biolog EcoPlates. We detected also a significant alteration in enzyme activity. The activity of enzymes responsible for depolymerization of complex organic matter was in a dose-dependent manner increased, whereas the highest activity reach samples amended with AgNPs at 100 mg kgdw−1. All these changes result in the accumulation of simple organic matter, which could increase osmotic pressure and have severe consequences on soil fertility. In amended soils, we detected alterations of activity of plant growth-promoting bacteria, specifically in the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylic acid deaminase, and siderophores. All these activities are related to mitigating abiotic stress. The presence of plants in experimental soil had both a mitigating and deepening effect on the toxicity of AgNPs. Both effects probably relate to the influence of AgNPs on the selection of different microbial communities in the soil and the “soil-plant” system.

Grazing accelerates labile and recalcitrant soil carbon loss driving by rare microbial taxa in a desert steppe

AbstractLivestock grazing in grasslands regulates the multifunctionality of those ecosystems and has an adverse effect on soil carbon (C) dynamics and fractions. However, our understanding of grazing‐induced changes in soil microbial community and their links to soil organic C (SOC) fractions is limited. By using a long‐term grazing experiment in desert steppe, we examined impacts of different grazing intensity on the diversity and composition of soil microbial community and their potential contribution to SOC content and fractions. The results showed that 15‐year grazing reduced total SOC (TSOC), albeit not significant, but induced a notable decrease in both labile and recalcitrant SOC fractions, especially under high grazing intensity. Soil prokaryotic communities were not significantly impacted by grazing intensity. However, we observed that sensitive operational taxonomic units (OTUs), identified by indicator taxa analysis, grouped in distinct modules that reflected the different grazing intensities, suggesting that groups of microbes may cluster together and respond to grazing intensity. Association networks of prokaryotic OTUs and organic C fractions showed that SOC fractions were significantly related to rare taxa, indicating that grazing practice may act as a kind of environmental filtering and strongly affected soil microbial rare taxa and thereafter SOC fractions. Together, our findings suggest that grazing intensity did not change total microbial community and TSOC but affected SOC fractions by altering rare taxa. Overall, our results indicated that soil C fractions and rare microbial taxa were more sensitive to grazing intensity, which could act as indicator of variations in ecosystem functions in the semi‐arid desert steppe.

Chiral enantiomers of the plant growth regulator paclobutrazol selectively affect community structure and diversity of soil microorganisms

Paclobutrazol is a triazole plant growth regulator with a wide range of applications in crop and fruit tree production. Paclobutrazol is used as a racemic mixture in agriculture. However, the effects of paclobutrazol enantiomers on soil microbial community structure and diversity are unclear. In the present study, Illumina high-throughput sequencing was used to study the enantioselective effects of two paclobutrazol enantiomers on soil microbial community. S-paclobutrazol was more persistent than R-paclobutrazol. The half-lives of the S- and R-isomers were 80 d and 50 d, respectively. No interconversion between the two isomers occurred in soils. In addition, the enantiomers had significant enantiomeric effects on soil microbial community and the paclobutrazol degradation was probably attributed to the presence of Pseudomonas and Mycobacterium. Notably, the relative abundance of Fusarium, a genus of filamentous fungi producing gibberellins, could be enantioselectively affected by the chiral enantiomers. Paclobutrazol enantiomers exhibited greater effects on the fungal community structure than bacterial community structure due to the fungicidal activity of paclobutrazol. Finally, R-paclobutrazol had a significant effect on the microbial networks. The findings of the present study suggest that the use of S-paclobutrazol may accomplish both plant growth regulation and the minimization of effects of paclobutrazol on soil microbial communities.

Biochar application enhances microbial interactions in mega-aggregates of farmland black soil

Soil microbial community diversity and composition are responsive to biochar application. However, the impacts of biochar application on soil microbial community structure and interactions in different aggregate fractions are poorly understood. We conducted a 3-year field trial involving biochar application to black soil in northeastern China. Four biochar treatments were applied: 0 (B0, control), 10 (B10), 30 (B30) and 50 (B50) t ha−1 biochar. Compared to the B0 treatment, biochar application significantly decreased the diversity of bacterial and fungal communities. In addition, biochar application significantly increased the relative abundances (RAs) of Bacteroidetes and Proteobacteria and significantly decreased those of Actinobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia. Moreover, the B30 and B50 treatments significantly increased and decreased the RA of Nitrospirae, respectively. Moreover, the RA trends of Acidobacteria, Nitrospirae and Planctomycetes among different aggregate fractions was mega-aggregates (ME; > 2 mm) > macroaggregates (MA; 0.25–2 mm) > microaggregates (MI; < 0.25 mm); the RAs of Basidiomycota and Glomeromycota in ME were higher than those in MA and MI. The RA of Ascomycota in MI was the highest among the different aggregate fractions. The co-occurrence networks showed that the B30 treatment enhanced microbial interactions in terms of the number of links, average degree, and modularity, while the B50 treatment reduced these interactions. Additionally, co-inertia analysis demonstrated that the microbial interactions in ME were enhanced by biochar application. Thus, an appropriate biochar application (e.g., 30 t ha−1 used in the present study area) can enhance soil microbial interactions, especially in ME.

Variations in soil microbial communities in the sedge-dominated peatlands along an altitude gradient on the northern slope of Changbai Mountain, China

The mechanisms that shape soil microbes in peatlands along the altitude gradient remain unresolved due to limited data and inconsistent findings along different vertical vegetation belts from investigations. In this study, we present results of soil phospholipid fatty acids (PLFAs) profiles from an altitude gradient survey (300–1500 m) in Changbai Mountain aimed at determining the elevational patterns of soil microbial communities and their driving forces in the sedge-dominated peatlands. The results showed that the total microbial lipid biomass in the sedge-dominated peatlands increased with altitude. However, there were no obvious trends with altitude in ratios of the fungi to bacteria (F/B), the Gram positive bacteria to Gram negative bacteria (G+/G-), and the bacteria to actinomycetes (B/ACT). Redundancy analysis indicated that the dissolved organic carbon (DOC) explained most variation in soil microbial groups, while mean annual temperature (MAT) explained most variation in microbial community structure. Variation partitioning analysis revealed that climatic factors had greater influences on soil microbial community structure than soil physical and chemical properties, and 53% of the total variance was explained by MAT, mean annual precipitation (MAP) and their combined effects. This finding challenges the prevailing view that local soil properties, but not climate, control soil microbial community structure along the altitude gradient, and enhances our understanding of the role of soil microbes as carbon pumps in sedge-dominated peatlands in the process of global warming.

Soil microbial functional diversity responses to different vegetation types in the Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve

PurposeThe soil microbial community is an important bioactive component of terrestrial ecosystems. Its structural and functional diversity directly affects carbon and nitrogen processes. This study aimed to investigate the variations in the functional diversity of soil microbial communities in forests with different types of vegetation.MethodsWe selected three typical vegetation types, larch (LG), black birch (BD), and larch and black birch mixed (LGBD) forests, located in the Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve. The Biolog-Eco microplate technology was selected to perform these analyses.ResultOur results showed clear differences between microorganisms in the three typical forests. The average well colour development (AWCD) change rate gradually increased with incubation time. The BD type had the highest AWCD value, followed by LGBD; the LG forest type had the lowest value. The difference in the soil microbial alpha diversity index between BD and LG was significant. A principal component analysis showed that PC1 and PC2 respectively explained 62.77% and 13.3% of the variance observed. The differences in the soil microbial carbon-source utilisation patterns under different vegetation types were mainly caused by esters and carbohydrates. Redundancy analysis showed that soil microbial functional diversity was strongly affected by soil physicochemistrical properties (e.g. organic carbon, total nitrogen and pH).ConclusionThese results provide a reference for further exploring the relationship between forest communities and soil microbes during the process of forest succession.

Soil properties and microbial community in the rhizosphere of Populus alba var. pyramidalis along a chronosequence

By maintaining soil structure and quality, soil microbial communities usually play important role in many forest ecosystem processes, including ecological succession. Understanding changes in the microbial communities of areas afforested with stands of different ages is of interest in ecology. Populus alba var. pyramidalis Bunge has been widely planted in Northwest China for ecological restoration. Rhizospheric soil samples were collected from 4-, 9-, 15-, 25- and 30-year-old plantations of P. alba to measure soil characteristics and soil microbial community diversity using Illumina MiSeq sequencing. The soil nutrition concentration and enzymatic activities decreased with depth of soil layer increased. In terms of stand age, alkaline phosphatase and dehydrogenase and the contents of nitrate N, available P and soil organic content (SOC) increased gradually. According to Illumina MiSeq sequencing results, the fungal and bacterial community structure varied with stand age, and diversity of fungi was less than bacteria. With increasing stand age, fungal community diversity indexes first increased and then decreased, peaked at 25y or 30y. RDA results suggested that soil available P and nitrate N were the most important factors governing fungal community structure, while available P contributed significantly to the variance of the bacterial community. Structural equation modelling (SEM) results indicated soil available P, nitrate N and SOC contents largely explained the shift in the microbial community structure along the cultivation chronosequence, and soil enzyme activities were related with changes in microbial community. Our results illustrated that the successional changes in microbial communities in the P. alba plantations can largely be attributed to changes in soil nutrition level along the chronosequence.

Functional diversity of soil microbial communities in response to supplementing 50% of the mineral N fertilizer with organic fertilizer in an oat field

The effects of supplementing 50% of the mineral N fertilizer with organic fertilizer on the metabolism and diversity of soil microbial communities in an oat field were investigated using Biolog-Eco plates. The experiment consisted of five treatments: no fertilizer (CK), mineral N fertilizer applied at 90 and 45 kg ha−1 N in the form of urea (U1 and U2, respectively), and U2 supplemented with organic fertilizer in the form of sheep manure at 90 and 45 kg ha−1 N (U2OM1 and U2OM2, respectively). Each treatment had three replications. The experiment was conducted in 2018 and 2019 in Pinglu District, Shanxi Province, China. The carbon source utilization by soil microbial communities, such as amino acids, amines, carbohydrates, carboxylic acids, and polymers, increased when 50% of the mineral N fertilizer was replaced with organic fertilizer in both years. This result was accompanied by increased richness, dominance, and evenness of the microbial communities. The utilization of amino acid, amine, and carboxylic acid carbon sources and community evenness were further improved when the organic fertilizer amount was doubled in both years. Biplot analysis indicated that amines and amino acids were the most representative of the total carbon source utilization by the soil microbial communities in both years. The highest oat yield was achieved at a total N application rate of 135 kg ha−1 in the treatment involving 45 kg ha−1 N in the form of urea and 90 kg ha−1 N in the form of sheep manure in both years. It was concluded that the application of 50% of the conventional rate of mineral N fertilizer supplemented with an appropriate rate of organic fertilizer enhanced both the functional diversity of soil microbial communities and oat yield. Amine and amino acid carbon sources may be used as a substitute for total carbon sources for assessing total carbon source utilization by soil microbial communities in oat fields in future studies.

The response of soil microbial communities to the infection of kauri (Agathis australis) seedlings with Phytophthora agathidicida

AbstractNew Zealand's ancient kauri (Agathis australis) forests are under threat from the spread of dieback disease, caused by the soil‐borne pathogen Phytophthora agathidicida. Characterizing the response of the soil microbiota to the infection of kauri with P. agathidicida is essential to identify how they may form a protective response to pathogen invasion and disease expression. This study infected 18‐month‐old kauri seedlings with a standardized inoculum load of P. agathidicida for 6 weeks under controlled environmental conditions. Following this, changes in the diversity, composition and biomass of soil microbial communities associated with kauri seedlings were characterized using high‐throughput 16S rRNA and ITS gene region sequencing and phospholipid fatty acid analysis. Significant differences were found in the composition of soil bacterial communities associated with inoculated and non‐inoculated kauri seedlings. Furthermore, soils of inoculated seedlings had a significantly higher relative abundance of bacteria previously reported to be associated with plant disease suppression, which included several members of the Firmicutes. Significant reductions were found in the fungal: bacterial biomass of soils from inoculated seedlings. This finding contrasts to previous field‐based research that observed an increased diversity of soil fungal communities associated with diseased kauri in old growth kauri forests. Further research that aims to isolate members of the kauri soil microbiota and study their interactions with P. agathidicida is required for us to begin selecting potential biocontrol agents against kauri dieback.

Variation in Soil Microbial Communities Along an Elevational Gradient in Alpine Meadows of the Qilian Mountains, China.

Bacterial, archaeal, and eukaryota diversity in mountainous areas varies along elevational gradients, but details remain unclear. Here, we use a next-generation sequencing method based on 16S/18S rRNA to reveal the soil microbial diversity and community compositions of alpine meadow ecosystems along an elevation span of nearly 2,000 m (1,936–3,896 m) in China’s Qilian Mountains. Both bacterial and eukaryota diversity increased linearly with increasing elevation, whereas archaeal diversity increased, but not significantly. The diversity patterns of several phyla in the bacterial, archaeal, and eukaryota communities were consistent with the overall elevational trend, but some phyla did not follow this pattern. The soil microbial community compositions were shaped by the coupled effects of regional climate and local soil properties. Intradomain links were more important than interdomain links in the microbial network of the alpine meadows, and these links were mostly positive. The bacteria formed more connections than either archaea or eukaryota, but archaea may be more important than bacteria in building the soil microbial co-occurrence network in this region. Our results provide new visions on the formation and maintenance of soil microbial diversity along an elevational gradient and have implications for microbial responses to climate change in alpine ecosystems.

Can the multi-walled carbon nanotubes be used to alleviate the phytotoxicity of herbicides in soils?

Herbicides are commonly used globally. However, residual herbicides in soils for ages often result in phytotoxicity and serious yield loss to subsequent crops. In this paper, the multi-walled carbon nanotubes (MWCNTs) were utilized to amend the herbicide polluted soil, and the adsorption performance of herbicides to MWCNTs amended soil was studied. Results indicate efficient alleviation of herbicide-induced phytotoxicity to rice and tobacco due to MWCNTs amendment. When 0.4% MWCNTs were applied, the concentration of sulfentrazone that inhibited the same rice height by 50% (IC50) increased to more than 3 times that of pure soil. When the MWCNTs were used to alleviate the phytotoxicity of quinclorac to tobacco, the MWCNTs not only alleviated the phytotoxicity of quinclorac but also promoted the growth of tobacco. The MWCNTs amended soil significantly increased the adsorption of herbicide to soil than biochar. The soil microbial analysis shows that MWCNTs had no significant effect on soil microbial community diversity, but the long-term exposure to MWCNTs could change the structure of the soil microbial community. Above all, our results highlighted the potential implication of the MWCNTs to ensure crop production by promoting crop growth and reducing the residual bioavailability of herbicides.

Long-term conversion from rice-wheat to rice-vegetable rotations drives variation in soil microbial communities and shifts in nitrogen-cycling through soil profiles

Land-use change (LUC) caused by agricultural intensification has aggravated soil reactive nitrogen (Nr) pollution in global rice agroecosystems. Microorganisms mediate Nr transformation; however, the structural and functional responses of the microbial community to LUC and soil Nr loading have yet to be synthesized. Simultaneously, rice–wheat (RW) rotations in China have been subjected to high rates of LUC, primarily to intensive rice-vegetable (RV) rotations. Here, 16S rRNA gene sequencing coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) was performed to assess the influence of conversion from RW to RV on soil Nr fractions, microbial communities, and N-cycling genes, especially over longer time scales and at deeper soil depths. Compared to RW, bacterial alpha-diversity increased in the 10-year RV, whereas archaeal alpha-diversity decreased with increasing years under RV rotations. Microbial beta-diversity significantly decreased after the conversion from RW to RV rotations, resulting in reduced heterogeneity in community structure (composition and abundance) across 0–40 cm soil profiles in RV rotations. Redundancy analysis suggested that this homogenization was driven by increased concentrations of nitrate N and decreased soil pH and soluble organic N concentrations in the RV. At 0–20 cm, RV decreased the abundance of Geobacter spp., Candidatus_Nitrosotalea spp., and their related N-fixation genes, whereas it increased the abundance of Streptomyces spp. and their related nitrification genes. Moreover, the 20-year RV significantly increased the potential denitrification and N2O emissions from soil at 0–40 cm by decreasing the abundance of bacterial nosZ genes (encoding nitrous-oxide reductase) and increasing archaeal nirK, nirS (nitrite reductase) genes, and bacterial norB and norC genes (nitric-oxide reductase). Collectively, RW-to-RV conversion decreased soil microbial diversity and increased the size of denitrification/N2O-producing communities, this homogenization of microbiomes in long-term RV system may be a potential source of N2O.

Effects of Soil Properties and Plant Diversity on Soil Microbial Community Composition and Diversity during Secondary Succession

Soil microbial communities play an important role in maintaining the ecosystem during forest secondary succession. However, the underlying mechanisms that drive change in soil microbial community structures during secondary succession remain poorly defined in species-rich subtropical coniferous forests. In this study, Illumina high-throughput sequencing was used to analyze the variations in soil microbial community structures during forest secondary succession in subtropical coniferous forests in China. The role of soil properties and plant diversity in affecting soil bacterial and fungal communities was determined using random forest and structural equation models. Highly variable soil microbial diversity was observed in different stages of secondary succession. Bacterial community diversity rose from early to middle and late successional stages, whereas fungal community diversity increased from early to middle successional stages and then declined in the late stage. The relative abundance of Acidobacteria, Gemmatimonadetes, Eremiobacterota(WPS-2), Rokubacteria, and Mortierellomycota increased during succession, whereas the relative abundance of Ascomycota and Mucoromycota decreased. The community composition and diversity of the soil microbial community were remarkably influenced by plant diversity and soil properties. Notably, tree species richness (TSR) displayed a significant and direct correlation to the composition and diversity of both bacterial and fungal communities. The carbon-to-nitrogen (C:N) ratio had a direct impact on the bacterial community composition and diversity, and pH had a marked impact on the fungal community composition and diversity. Furthermore, succession stage and plant diversity indirectly impacted the composition and diversity of soil bacterial and fungal communities via soil properties. Overall, it can be concluded that soil intrinsic properties and plant diversity might jointly drive the changes in soil microbial community composition and diversity during secondary succession of subtropical coniferous forests.

Lycium barbarum L. (goji berry) monocropping causes microbial diversity loss and induces Fusarium spp. enrichment at distinct soil layers

The high salt- and drought-tolerance of Lycium barbarum L. (goji berry) makes the plant suitable for cultivation in the arid and semi-arid regions of northwest China. However, monocropping of L. barbarum has caused severe issues, including increasing plant disease incidents and declining goji berry productivity. The negative impacts of L. barbarum monocropping on the soil health over time remain unclear. We investigated the temporal shifts in soil properties and microbial community diversity in the top (0–20 cm) and subsoils (20–40 cm) of L. barbarum fields across a 20-year age sequence and the adjacent control fields at two independent research sites in Ningxia, China. Our results show that L. barbarum monocropping leads to accumulation of total organic C, N, P, and available N stocks, but simultaneously caused secondary soil salinization and soil pH declination. The community α-diversity indices and the dissimilarities in community compositions of bacteria and fungi generally decline with the increase in stand age at both soil depths. Co-occurrence analysis found a decreased complexity of network structure with stand development, indicating that monocropping would profoundly disrupt the potential interactions among soil microbes. The phytopathogenic fungi Fusarium spp. progressively prevailed in soils of L. barbarum fields. The structural equation modeling further demonstrates that the variation in bacterial community composition directly explained the increase in the absolute abundance of Fusarium spp. The results infer an essential role of soil bacterial assemblages in the biocontrol of Fusarium wilt of L. barbarum under monocropping. Together, our results suggest that secondary soil salinization, loss of soil microbial diversity, and build-up of fungal phytopathogens, particularly in subsoils, are major threats to the soil health of L. barbarum field. An in-depth understanding of these threats to soil quality could help develop sustainable cropping management for L. barbarum.

The response of soil microbial communities to soil erodibility depends on the plant and soil properties in semiarid regions

AbstractNatural succession and afforestation are the two main restoration methods of degraded soil in semiarid and arid regions. Up to now, the soil microbial communities and their roles in soil erodibility have been unclear. Our work aimed to evaluate the effects of ecological restoration on the diversity and composition of soil microbial communities at depths of 0–20 cm and their interaction with soil erodibility. Four main restoration types, natural succession land andPinus tabuliformis,Armeniaca sibirica, andRobinia pseudoacaciaplantations were chosen. Restoration with different vegetation communities decreased the soil erodibilityK‐factor (K) by 13.37–20.64%. Proteobacteria, Acidobacteria, and Actinobacteria were dominant bacterial phyla at all sites. The dominant fungal phyla were Basidiomycota, Ascomycota, and Zygomycota. However, there were obvious differences in bacterial and fungal communities among restoration types due to variations in plant and soil properties. Redundancy analysis showed that the soil microbial communities explained 67.30% of the total variance in soil erodibility. Bacterial communities mainly affect the microaggregate formation, whereas fungal communities have a greater effect on macroaggregate formation. Additionally, the structural equation modeling also suggests that vegetation characteristics, soil organic carbon, and fungal communities, and macroaggregates (&gt; 5 mm) have positive effects on mean weight diameter. Therefore, the combination of vegetation community, soil properties, and microbial communities improves the soil structure against erosion in this area.

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.

Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.