Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study

Long-term agricultural cultivation decreases microbial nutrient limitation in coastal saline soils

Soil enzyme activities are pivotal for diverse biochemical processes and are sensitive to land use changes. They can indicate soil microbial nutrient limitations. Nonetheless, the mechanism governing the response of soil microbial nutrient limitation to land use alterations in coastal regions remains elusive. We assessed soil nutrients, microbial biomass, and extracellular enzyme activities across various land use types-natural (wasteland and woodland) and agricultural (farmland and orchard)-in the Hangzhou Bay area, China. All four land use types experience co-limitation by carbon (C) and phosphorus (P). However, the extent of microbial resource limitations varies among them. Long-term agricultural practices diminish microbial C and P limitations in farmland and orchard soils compared to natural soils, as evidenced by lower ecoenzymatic C:N ratios and vector lengths, alongside higher microbial carbon use efficiency (CUE). Soil nutrient stoichiometric ratios and CUE are primary factors influencing microbial C and P limitations. Thus, fostering appropriate land use and management practices proves imperative to regulate soil nutrient cycles and foster the sustainable management of coastal areas.

Multitrophic Diversity of the Biotic Community Drives Ecosystem Multifunctionality in Alpine Grasslands

Biodiversity and ecosystem multifunctionality are currently hot topics in ecological research. However, little is known about the role of multitrophic diversity in regulating various ecosystem functions, which limits our ability to predict the impact of biodiversity loss on human well-being and ecosystem multifunctionality. In this study, multitrophic diversity was divided into three categories: plant, animal, and microbial communities (i.e., plant diversity, rodent diversity, and bacterial and fungal diversity). Also, 15 ecosystem functions were divided into four categories-water conservation, soil fertility, nutrient cycling and transformation, and community production-to evaluate the significance of biotic and abiotic variables in maintaining ecosystem multifunctionality. Results indicated that species diversity at multiple trophic levels had a greater positive impact on ecosystem multifunctionality than species diversity at a single trophic level. Notably, the specific nature of this relationship depended on the niche breadths of plants, indicating that plants played a key role in linking above and belowground trophic levels. Abiotic factors such as altitude and pH directly acted on ecosystem multifunctionality and could explain changes in ecosystem functions. Overall, our study offers valuable insights into the critical role of multitrophic species diversity in preserving ecosystem multifunctionality within alpine grassland communities, as well as strong support for the importance of biodiversity protection.

Identification of the regulatory roles of water qualities on the spatio-temporal dynamics of microbiota communities in the water and fish guts in the Heilongjiang River

The Heilongjiang River is one of the largest rivers in the cool temperate zone and has an abundant fish source. To date, the microbiota community in water samples and fish guts from the Heilongjiang River is still unclear. In the present study, water samples and fish guts were collected from four locations of the Heilongjiang River during both the dry season and the wet season to analyze the spatio-temporal dynamics of microbiota communities in the water environment and fish guts through 16s ribosome RNA sequencing. The water qualities showed seasonal changes in which the pH value, dissolved oxygen, and total dissolved solids were generally higher during the dry season, and the water temperature was higher during the wet season. RDA indicated that higher pH values, dissolved oxygen, and total dissolved solids promoted the formation of microbiota communities in the water samples of the dry season, while higher water temperature positively regulated the formation of microbiota communities in the water samples of the wet season. LEFSe identified five biomarkers with the most abundant difference at the genus level, of which TM7a was upregulated in the water samples of the dry season, and SM1A02, Rheinheimera, Gemmatimonas, and Vogesella were upregulated in the water samples of the wet season. Pearson analysis revealed that higher pH values and dissolved oxygen positively regulated the formation of TM7a and negatively regulated the formation of SM1A02, Rheinheimera, Gemmatimonas, and Vogesella (p < 0.05), while higher water temperature had the opposite regulatory roles in the formation of these biomarkers. The relative abundance of microbiota diversity in fish guts varies greatly between different fish species, even if the fishes were collected from the same water source, indicating that dietary habits and fish species may be key factors, affecting the formation and construction of microbiome community in fish gut. P. glenii, P. lagowskii, G. cynocephalus, and L. waleckii were the main fish resources, which were collected and identified from at least six sample points. RDA indicated that the microbiota in the water environment regulated the formation of microbiota community in the guts of G. cynocephalus and L. waleckii and had limited regulated effects on P. glenii and P. lagowskii. The present study identified the regulatory effects of water qualities on the formation of microbiota communities in the water samples and fish guts, providing valuable evidence for the protection of fish resources in the Heilongjiang River.

Shifts in fungal community diversity and potential function under natural forest succession and planted forest restoration in the Kunyu Mountains, East China

Soil fungi participate in various ecosystem processes and are important factors driving the restoration of degraded forests. However, little is known about the changes in fungal diversity and potential functions under the development of different vegetation types during natural (secondary forest succession) and anthropogenic (reforestation) forest restoration. In this study, we selected typical forest succession sequences (including Pinus densiflora Siebold & Zucc., pine-broadleaf mixed forest of P. densiflora and Quercus acutissima Carruth., and Q. acutissima), as well as natural secondary deciduous broadleaved mixed forests and planted forests of Robinia pseudoacacia on Kunyu Mountain for analysis. We used ITS rRNA gene sequencing to characterize fungal communities and used the FUNGuild database to predict fungal functional groups. The results showed that forest succession affected fungal β-diversity, but not the α-diversity. There was a significant increase in Basidiomycota and a decrease in Ascomycota in the later successional stage, accompanied by an increase in the functional groups of ectomycorrhizal fungi (ECM). Conversely, planted forests exhibited decreased fungal α-diversity and altered community compositions, characterized by fewer Basidiomycota and more Ascomycota and Mucoromycota. Planted forests led to a decrease in the relative abundances of ECM and an increase in animal pathogens. The TK content was the major factor explaining the distinction in fungal communities among the three successional stages, whereas pH, AP, and NH4 + were the major factors explaining community variations between natural and planted forests. Changes in vegetation types significantly affected the diversity and functional groups of soil fungal communities during forest succession and reforestation, providing key insights for forest ecosystem management in temperate forests.

Nutrients addition decreases soil fungal diversity and alters fungal guilds and co-occurrence networks in a semi-arid grassland in northern China

Anthropogenic eutrophication is known to impair the diversity and stability of aboveground community, but its effects on the diversity, composition and stability of belowground ecosystems are not yet fully understood. In this study, we conducted a 9-year nitrogen (N) and phosphorus (P) addition experiment in a semi-arid grassland of Northern China to elucidate the impacts of nutrients addition on soil fungal diversity, functional guilds, and co-occurrence networks. The results showed that N addition significantly decreased soil fungal diversity and altered fungal community composition, whereas P addition had no impact on them. The relative abundance of arbuscular mycorrhizal fungi and leaf_saprotroph were reduced by N and P addition, but P addition enhanced the abundance of saprotrophic fungi. Co-occurrence network analysis revealed that N addition destabilized fungal network complexity and stability, while P addition slightly increased the network complexity. Additionally, the network analysis of N × P interaction revealed that P addition mitigated negative effects of N addition on network complexity and stability. Structural equation modeling (SEM) results suggested that nutrients addition directly or indirectly influenced the fungal community structure through the loss of plant richness and the increase of perennial grass biomass. These findings indicate that in comparison to P addition, N addition exhibits a pronounced negative effect on soil fungal communities. Our findings also suggest that changes in plant functional groups under nutrients deposition are pivotal in shaping soil fungal community structure in semi-arid grassland and highlight the need for a better understanding of the belowground ecosystem dynamics.

Interplay between edaphic and climatic factors unravels plant and microbial diversity along an altitudinal gradient

Altitude influences biodiversity and physiochemical soil attributes in terrestrial ecosystems. It is of immense importance to know the patterns of how interactions among climatic and edaphic factors influence plant and microbial diversity in various ecosystems, particularly along the gradients. We hypothesize that altitudinal variation determines the distribution of plant and microbial species as well as their interactions. To test the hypothesis, different sites with variable altitudes were selected. Analyses of edaphic factors revealed significant (p < 0.001) effects of the altitude. Soil ammonium and nitrate were strongly affected by it contrary to potassium (K), soil organic matter and carbon. The response patterns of individual taxonomic groups differed across the altitudinal gradient. Plant species and soil fungal diversity increased with increasing altitude, while soil archaeal and bacterial diversity decreased with increasing altitude. Plant species richness showed significant positive and negative interactions with edaphic and climatic factors. Fungal species richness was also significantly influenced by the soil ammonium, nitrate, available phosphorus, available potassium, electrical conductivity, and the pH of the soil, but showed non-significant interactions with other edaphic factors. Similarly, soil variables had limited impact on soil bacterial and archaeal species richness along the altitude gradient. Proteobacteria, Ascomycota, and Thaumarchaeota dominate soil bacterial, fungal, and archaeal communities, with relative abundance of 27.4%, 70.56%, and 81.55%, respectively. Additionally, Cynodon dactylon is most abundant plant species, comprising 22.33% of the recorded plant taxa in various study sites. RDA revealed that these communities influenced by certain edaphic and climatic factors, e.g., Actinobacteria strongly respond to MAT, EC, and C/N ratio, Ascomycota and Basidiomycota show strong associations with EC and MAP, respectively. Thaumarcheota are linked to pH, and OM, while Cyperus rotundus are sensitive to AI and EC. In conclusion, the observed variations in microbial as well as plant species richness and changes in soil properties at different elevations provide valuable insights into the factors determining ecosystem stability and multifunctionality in different regions.

Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China

Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the "space instead of time" approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.

Seasonal linkages between soil nitrogen mineralization and the microbial community in broadleaf forests with Moso bamboo (Phyllostachys edulis) invasion

Plant invasions significantly alter the microbiome of the soil in terms of fungal and bacterial communities, which in turn regulates ecosystem processes and nutrient dynamics. However, it is unclear how soil microbial communities, nitrogen (N) mineralization, and their linkages respond to plant invasions over the growing season in forest ecosystems. The present study investigated the seasonal associations between the microbial composition/function and net N mineralization in evergreen broadleaf, mixed bamboo-broadleaf, and Moso bamboo (Phyllostachys edulis) forests, depicting uninvaded, moderately invaded, and heavily invaded forests, respectively. The ammonification and nitrification rates in the bamboo forest were significantly higher than those in the broadleaf and mixed bamboo-broadleaf forests during the spring season only. The forest type and seasonal variation significantly influenced the net rates of ammonification and nitrification and the abundances of bacterial apr and AOB amoA, fungal cbhI and lcc genes, as well as the microbial composition. Moreover, the partial least squares path model revealed that bamboo invasion enhanced net ammonification through increasing total N and fungal-to-bacterial ratio, and enhanced net nitrification through modifying the bacterial composition and increasing the fungal-to-bacterial ratio during spring. However, microbial parameters had no significant effect on net ammonification and nitrification during autumn. We conclude that shifts in the microbial abundance and composition following bamboo invasion facilitated soil N mineralization during spring, contributing to the rapid growth of Moso bamboo at the beginning of the growth season and its invasion into adjacent subtropical forests.

Litter decomposition and nutrient release are faster under secondary forests than under Chinese fir plantations with forest development

In terrestrial ecosystems, leaf litter is the main source of nutrients returning to the soil. Understanding how litter decomposition responds to stand age is critical for improving predictions of the effects of forest age structure on nutrient availability and cycling in ecosystems. However, the changes in this critical process with stand age remain poorly understood due to the complexity and diversity of litter decomposition patterns and drivers among different stand ages. In this study, we examined the effects of stand age on litter decomposition with two well-replicated age sequences of naturally occurring secondary forests and Chinese fir (Cunninghamia lanceolata) plantations in southern China. Our results showed that the litter decomposition rates in the secondary forests were significantly higher than those in the Chinese fir plantations of the same age, except for 40-year-old forests. The litter decomposition rate of the Chinese fir initially increased and then decreased with stand age, while that of secondary forests gradually decreased. The results of a structural equation model indicated that stand age, litter quality and microbial community were the primary factors driving nutrient litter loss. Overall, these findings are helpful for understanding the effects of stand age on the litter decomposition process and nutrient cycling in plantation and secondary forest ecosystems.

Divergent linkages of soil phosphorus fractions to edaphic properties following afforestation in the riparian zone of the upper Yangtze river, China

Soil phosphorus (P) is an essential nutrient element for plant growth but it is also one of the elements of agricultural-dominated watershed pollution. While the vegetation in the riparian zone usually plays an important role in regulating P pollutants. However, how afforestation affects soil P dynamics and fractions in the riparian zone remains largely unclear. Here, we investigated soil P fractions, and associated drivers including edaphic properties, microbial attributes, and soil enzyme activities under conversion from cropland to different afforested lands in order to better understand the dynamics of soil P fractions in the riparian zone of the upper Yangtze River. We found that afforestation significantly decreased the concentrations of available phosphorus, microbial biomass P, and labile P fractions, but the moderately labile P and Stable P did not significantly differ among afforestation types. Particularly, the lowest concentration of labile P was observed in Morus alba (M.a.) forests followed by the Salix babylonica (S.b.) forests, whereas croplands generally exhibited an inverse trend with a higher labile P concentration compared to woodlands, especially in croplands nearby Morus alba forests. Generally, P fractions were negatively associated with soil pH and C:N ratio, while positively related to microbial attributes, N:P ratio, and alkaline phosphatase activities. The labile P and moderately labile P fractions were predominantly regulated by biotic factors (i.e., microbial biomass P, microbial biomass N, leucine amino peptidase), whereas the stable P was strongly related to abiotic factors (i.e., total C concentration, pH, C:N ratio). These findings indicate afforestation is conducive to intercept more labile P, resulting in reduced P leaching to rivers. Collectively, our results not only offer direct experimental insight into predicting the effects of afforestation on soil P fractions but also have important implications for agricultural pollution management and reforestation strategies in the riparian zone.

Mechanisms underlying the succession of plant rhizosphere microbial community structure and function in an alpine open-pit coal mining disturbance zone

Elucidating the responses and potential functions of soil microbial communities during succession is important for understanding biogeochemical processes and the sustainable development of plant communities after environmental disturbances. However, studies of such dynamics during post-mining ecological restoration in alpine areas remain poorly understood. Microbial diversity, nitrogen, and phosphorus cycle functional gene potential in the Heishan mining area of Northwest China was studied, including primitive succession, secondary succession, and artificial succession disturbed by mining. The results revealed that: (1) The dominant bacteria in both categories (non-remediated and ecologically restored) of mining area rhizosphere soil were Proteobacteria, adopting the r strategy, whereas in naturally occurring soil outside the mining area, the dominant bacteria were actinomycetes and Acidobacteria, adopting the k strategy. Notably, mining perturbation significantly reduced the relative abundance of archaea. (2) After restoration, more bacterial network node connections were observed in mining areas than were originally present, whereas the archaeal network showed the opposite trend. (3) The networks of microbial genes related to nitrogen and phosphorus cycle potential differed significantly, depending on the succession type. Namely, prior to restoration, there were more phosphorus related functional gene network connections; these were also more strongly correlated, and the network was more aggregated. (4) Soil factors such as pH and NO₃-N affected both the mining area remediation soil and the soil outside the mining area, but did not affect the soil of the original vegetation in the mining area. The changes in the structure and function of plant rhizosphere microorganisms after mining disturbance can provide a theoretical basis for the natural restoration of mining areas.

Oxygen availability regulates the quality of soil dissolved organic matter by mediating microbial metabolism and iron oxidation

Dissolved organic matter (DOM) plays a vital role in biogeochemical processes and in determining the responses of soil organic matter (SOM) to global change. Although the quantity of soil DOM has been inventoried across diverse spatio-temporal scales, the underlying mechanisms accounting for variability in DOM dynamics remain unclear especially in upland ecosystems. Here, a gradient of SOM storage across 12 croplands in northeast China was used to understand links between DOM dynamics, microbial metabolism, and abiotic conditions. We assessed the composition, biodegradability, and key biodegradable components of DOM. In addition, SOM and mineral-associated organic matter (MAOM) composition, soil enzyme activities, oxygen availability, soil texture, and iron (Fe), Fe-bound organic matter, and nutrient concentrations were quantified to clarify the drivers of DOM quality (composition and biodegradability). The proportion of biodegradable DOM increased exponentially with decreasing initial DOM concentration due to larger fractions of depolymerized DOM that was rich in small-molecular phenols and proteinaceous components. Unexpectedly, the composition of DOM was decoupled from that of SOM or MAOM, but significantly related to enzymatic properties. These results indicate that microbial metabolism exhibited a dominant role in DOM generation. As DOM concentration declined, increased soil oxygen availability regulated DOM composition and enhanced its biodegradability mainly through mediating microbial metabolism and Fe oxidation. The oxygen-induced oxidation of Fe(II) to Fe(III) removed complex DOM compounds with large molecular weight. Moreover, increased oxygen availability stimulated oxidase-catalyzed depolymerization of aromatic substances, and promoted production of protein-like DOM components due to lower enzymatic C/N acquisition ratio. As global changes in temperature and moisture will have large impacts on soil oxygen availability, the role of oxygen in regulating DOM dynamics highlights the importance of integrating soil oxygen supply with microbial metabolism and Fe redox status to improve model predictions of soil carbon under climate change.

Forest succession improves the complexity of soil microbial interaction and ecological stochasticity of community assembly: Evidence from Phoebe bournei-dominated forests in subtropical regions

Forest succession is a central ecological topic, due to the importance of the associated dynamic processes for terrestrial ecosystems. However, very little is currently known about the community assembly and interaction of soil microbial communities along forest successional trajectories, particularly regarding the microbial community dynamics in contrasting seasons. To bridge these knowledge gaps, we studied soil bacterial and fungal community compositions, assemblages, and co-occurrence networks in a well-established successional gradient of Phoebe bournei-dominated forest, spanning about 65 years of forest development in a subtropical region. Illumina MiSeq sequencing of 16S and ITS genes was employed for the assessment of soil bacterial and fungal community composition and diversity, respectively. The relative abundance and α-diversity of soil bacteria and fungi showed a differential trend over forest succession. The dominant fungal phyla (Basidiomycota and Ascomycota) changed more frequently than the dominant bacterial phyla (Proteobacteria, Acidobacteriota, and Actinobacteriota), indicating that soil fungi have a more sensitive relationship with forest succession compared with bacteria. The soil microbial community variation induced by forest succession was significantly affected by soil total phosphorus, dissolved organic carbon content and pH. Compared to deterministic processes, stochastic processes mainly dominated the community assembly of soil microbial communities. Meanwhile, the relative importance of stochasticity in soil fungal communities increased in the later stages. In Particular, dispersal limitation and drift accounted for a large proportion of bacterial and fungal community assembly, respectively. In addition, the co-occurrence networks of soil microbial communities became more complex as succession proceeds. Soil bacteria and fungi exhibited more competition and cooperation along the forest successional gradient. Collectively, our findings suggest that forest succession improves the complexity of soil microbial interactions and the ecological stochasticity of community assembly in Phoebe bournei-dominated forests, providing key insights into the relationship between microbial communities and forest succession.

Spatial Heterogeneity of Soil Bacterial Community Structure and Enzyme Activity along an Altitude Gradient in the Fanjingshan Area, Northeastern Guizhou Province, China

Changes in altitude can cause regional microclimate changes, leading to the spatial heterogeneity of environmental factors and soil bacteria. However, the internal driving process and mechanism remain unclear. Here, we selected Fanjingshan, a typical nature reserve in the subtropical region of south China with a clear altitudinal belt, to reveal the response mechanisms of microbial populations with altitude changes. We examined the physiochemical and biological properties (pH and soil enzyme activities) of 0~10 cm soil layers, soil bacterial diversity, and community structure across the 2.1 km belt (consisting of six altitude ranges). Our results showed that soil pH was highest at the altitude range below 900 m and decreased with altitude thereafter. Soil enzyme activities showed an overall decreasing trend with altitude rising. The soil sucrase and catalase activity was highest (48.35 mg.g^-1.d^-1 and 23.75 µmol.g^-1, respectively) at altitudes below 900 m; the soil urease activity was highest (704.24 µg.g^-1.d^-1) at 900~1200 m; and the soil acid phosphatase activity was highest (57.18 µmol.g^-1) at 1200~1500 m. In addition, the soil bacterial community diversity showed a linear increasing trend, with the maximum abundance at 1500~1800 m. Soil pH was correlated with enzyme activity and bacterial community composition and structure, and the correlation was the strongest between pH and the distribution of bacterial diversity at altitudes below 900 m. Overall, soil enzyme activities and soil bacterial diversity showed spatial heterogeneity along the altitude gradient, and their community structure and composition were affected by altitude as a result of changes in soil physicochemical factors. This study provides a better and deeper understanding of the spatial succession of soil in the Fanjingshan area and the distribution pattern of soil microorganisms in central subtropical mountain ecosystems.

Temporal complementarity between roots and mycorrhizal fungi drives wheat nitrogen use efficiency

Improving nitrogen (N) use efficiency (NUE) to reduce the application of N fertilisers in a way that benefits the environment and reduces farmers' costs is an ongoing objective for sustainable wheat production. However, whether and how arbuscular mycorrhizal fungi (AMF) affect NUE in wheat is still not well explored. Three independent but complementary experiments were conducted to decipher the contribution of roots and AMF to the N uptake and utilisation efficiency in wheat. We show a temporal complementarity pattern between roots and AMF in shaping NUE of wheat. Pre-anthesis N uptake efficiency mainly depends on root functional traits, but the efficiency to utilise the N taken up during pre-anthesis for producing grains (E_N,g ) is strongly affected by AMF, which might increase the uptake of phosphorus and thereby improve photosynthetic carbon assimilation. Root association with AMF reduced the N remobilisation efficiency in varieties with high E_N,g ; whilst the overall grain N concentration increased, due to a large improvement in post-anthesis N uptake supported by AMF and/or other microbes. The findings provide evidence for the importance of managing AMF in agroecosystems, and an opportunity to tackle the contradiction between maximising grain yield and protein concentration in wheat breeding.

Determinants of Soil Bacterial Diversity in a Black Soil Region in a Large-Scale Area

Soils in black soil areas are high in organic matter and rich in nutrients. Soil microorganisms are particularly critical to cultivated land. The objective of this study was to explore the influencing factors of soil bacterial diversity under special regional conditions in a black soil region. In this study, the cultivated land in a black soil area was used as the study area and a random forest was used to map the bacterial abundance in the black soil area based on 1810 sample points. DbMEM analysis was used to quantify the spatial effect of the black soil area and to identify the influencing factors of soil bacterial abundance in the black soil area in combination with soil properties, terrain, and climate. Results of a variation division showed that broad (8.336%), AT (accumulated temperature, 5.520%), and pH (4.184%) were the main factors affecting soil bacterial diversity. The broad effect was more significant in the spatial effect, which may be related to the local landscape configuration. Overall, our research showed that the influencing factors of soil bacteria will be affected by regional characteristics.

Depth-dependent drivers of soil microbial necromass carbon across Tibetan alpine grasslands

Microbial necromass carbon (C) has been considered an important contributor to persistent soil C pool. However, there still lacks large-scale systematic observations on microbial necromass C in different soil layers, particularly for alpine ecosystems. Besides, it is still unclear whether the relative importance of biotic and abiotic variables such as plant C input and mineral properties in regulating microbial necromass C would change with soil depth. Based on the combination of large-scale sampling along a ~2200 km transect across Tibetan alpine grasslands and biomarker analysis, together with a global data synthesis across grassland ecosystems, we observed a relatively low proportion of microbial-derived C in Tibetan alpine grasslands compared to global grasslands (topsoil: 45.4% vs. 58.1%; subsoil: 41.7% vs. 53.7%). We also found that major determinants of microbial necromass C depended on soil depth. In topsoil, both plant C input and mineral protection exerted dominant effects on microbial necromass C. However, in subsoil, the physico-chemical protection provided by soil clay particles, iron-aluminum oxides, and exchangeable calcium dominantly facilitated the preservation of microbial necromass C. The differential drivers over microbial necromass C between soil depths should be considered in Earth system models for accurately forecasting soil C dynamics and its potential feedback to global warming.

Planting Systems Affect Soil Microbial Communities and Enzymes Activities Differentially under Drought and Phosphorus Addition

The use of phosphorus (P) to alleviate soil nutrient deficiency alters resources in plant and microbial communities, but it remains unknown how mixed and monospecific planting of forest tree species shape soil microbial structure and functions in response to drought and its interplay with phosphorus addition. We investigated the microbial structure and chemical properties of forest soils planted with P. zhennan monoculture, A. cremastogyne monoculture, and their mixed cultures. The three planting systems were exposed to drought (30-35% water reduction) and the combination of drought with P. A well-watered treatment (80-85% water addition) of similar combinations was used as the control. Planting systems shaped the effects of drought on the soil microbial properties leading to an increase in nitrate nitrogen, urease activity, and microbial biomass carbon in the monocultures, but decrease in mixed cultures. In the monoculture of P. zhennan, addition of P to drought-treated soil increased enzyme activities, the concentration of dissolved organic nitrogen, and carbon, leading to increase in the total bacteria, G⁺ bacteria, and arbuscular mycorrhizal fungi. Except in the drought with P addition treatment, the impact of admixing on total phospholipid fatty acids (PLFAs), bacterial PLFA, and fungi PLFA was synergistic in all treatments. Our findings indicated that in monoculture of P. zhennan and its mixed planting with A. cremastogyne, greater biological activities could be established under drought conditions with the addition of P.

Soil CO2 and CH4 emissions and their carbon isotopic signatures linked to saturated and drained states of the Three Gorges Reservoir of China

Human activities such as dams disturb the structure and function of wetlands, triggering large soil CO₂ and CH₄ emissions. However, controls over field CO₂ and CH₄ emissions and their carbon isotopic signatures in reservoir wetlands are not yet fully understood. We investigated in situ CO₂ and CH₄ emissions, the δ¹³C values of CO₂ and CH₄, and associated environments in the saturated and drained states under four elevations (i.e., the water column, <147 m, permanent inundation area without plants; the low, 145-160 m, frequently flooded area with revegetation; the high, 160-175 m, rarely flooded area with revegetation; and the upland area as the control, >175 m, nonflooded area with original plants) in the Three Gorges Reservoir area. The CO₂ emissions was significantly higher in high elevation, and they also significantly differed between the saturated and drained states. In contrast, the CH₄ emissions on average (41.97 μg CH₄ m^-2 h^-1) were higher at high elevations than at low elevations (22.73 μg CH₄ m^-2 h^-1) during the whole observation period. CH₄ emissions decreased by 90% at low elevations and increased by 153% at high elevations from the saturated to drained states. The δ¹³C of CH₄ was more enriched at high elevations than in the low and upland areas, with a more depleted level under the saturated state than under the drained state. We found that soil CO₂ and CH₄ emissions were closely related to soil substrate quality (e.g., C: N ratio) and enzyme activities, whereas the δ¹³C values of CO₂ and CH₄ were primarily associated with root respiration and methanogenic bacteria, respectively. Specifically, the effects of the saturated and drained states on soil CO₂ and CH₄ emissions were stronger than the effect of reservoir elevation, thereby providing an important basis for assessing carbon neutrality in response to anthropogenic activities.

The Mixed Addition of Biochar and Nitrogen Improves Soil Properties and Microbial Structure of Moderate-Severe Degraded Alpine Grassland in Qinghai-Tibet Plateau

The degradation of the grassland system has severely threatened the safety of the ecological environment and animal husbandry. The supplement of key substances lost due to degradation is widely used to accelerate the restoration of the degraded grassland ecosystem. In this study, we investigated the effects of biochar and nitrogen addition on soil properties and microorganisms of degraded alpine grassland. The experimental treatments consisted of the control without any addition, only nitrogen addition (10 gN/m²), only biochar addition (4.00 kg/m² biochar), and the mixed addition of biochar and nitrogen (4.00 kg/m² biochar and 10 gN/m² nitrogen, respectively). Adding N alone did not significantly change the pH, total organic carbon (TOC), total nitrogen (TN), microbial biomass (MB), and the composition proportion of microbes of the soil, but increased the contents of soil water content (SWC), NH₄ ⁺-N, NO₃ ^--N, available phosphorus (AP), and the biomass of bacteria and fungi. The addition of biochar or the mixture of biochar and nitrogen increased the contents of pH, TOC, TN, MB, SWC, NH₄ ⁺-N, NO₃ ^--N, AP, bacteria, and fungi in the soil and changed the structure of the soil microbial community. The increasing intensity of AP, bacteria, and fungi under the addition of biochar or the mixture of biochar and nitrogen was significantly greater than that under N addition alone. These results indicated that the separated addition of nitrogen and biochar and the mixed addition of biochar and nitrogen all improved the soil condition of the moderate-severe degraded alpine grassland, but the mixed addition of biochar and nitrogen could be a better strategy to remediate the degraded alpine grassland.

Differential response of soil CO2 , CH4 , and N2 O emissions to edaphic properties and microbial attributes following afforestation in central China

Land use change specially affects greenhouse gas (GHG) emissions, and it can act as a sink/source of GHGs. Alterations in edaphic properties and microbial attributes induced by land use change can individually/interactively contribute to GHG emissions, but how they predictably affect soil CO₂ , CH₄ , and N₂ O emissions remain unclear. Here, we investigated the direct and indirect controls of edaphic properties (i.e., dissolved organic carbon [DOC], soil organic C, total nitrogen, C:N ratio, NH4+ -N, NO3- -N, soil temperature [ST], soil moisture [SM], pH, and bulk density [BD]) and microbial attributes (i.e., total phospholipid fatty acids [PLFAs], 18:1ω7c, nitrifying genes [ammonia-oxidizing archaea, ammonia-oxidizing bacteria], and denitrifying genes [nirS, nirK, and nosZ]) over the annual soil CO₂ , CH₄ , and N₂ O emissions from the woodland, shrubland, and abandoned land in subtropical China. Soil CO₂ and N₂ O emissions were higher in the afforested lands (woodland and shrubland) than in the abandoned land, but the annual cumulative CH₄ uptake did not significantly differ among all land use types. The CO₂ emission was positively associated with microbial activities (e.g., total PLFAs), while the CH₄ uptake was tightly correlated with soil environments (i.e., ST and SM) and chemical properties (i.e., DOC, C:N ratio, and NH4+ -N concentration), but not significantly related to the methanotrophic bacteria (i.e., 18:1ω7c). Whereas, soil N₂ O emission was positively associated with nitrifying genes, but negatively correlated with denitrifying genes especially nosZ. Overall, our results suggested that soil CO₂ and N₂ O emissions were directly dependent on microbial attributes, and soil CH₄ uptake was more directly related to edaphic properties rather than microbial attributes. Thus, different patterns of soil CO₂ , CH₄ , and N₂ O emissions and associated controls following land use change provided novel insights into predicting the effects of afforestation on climate change mitigation outcomes.

Soil enzyme responses to land use change in the tropical rainforest of the Colombian Amazon region

Soil enzymes mediate key processes and functions of the soils, such as organic matter decomposition and nutrient cycling in both natural and agricultural ecosystems. Here, we studied the activity of five extracellular soil enzymes involved in the C, N, and P-mineralizing process in both litter and surface soil layer of rainforest in the northwest region of the Colombian Amazon and the response of those soil enzymes to land use change. The experimental study design included six study sites for comparing long-term pasture systems to native forest and regeneration practices after pasture, within the main landscapes of the region, mountain and hill landscapes separately. Results showed considerable enzymatic activity in the litter layer of the forest, highlighting the vital role of this compartment in the nutrient cycling of low fertility soils from tropical regions. With the land use transition to pastures, changes in soil enzymatic activities were driven by the management of pastures, with SOC and N losses and reduced absolute activity of soil enzymes in long-term pastures under continuous grazing (25 years). However, the enzyme activities expressed per unit of SOC did not show changes in C and N-acquiring enzymes, suggesting a higher mineralization potential in pastures. Enzymatic stoichiometry analysis indicated a microbial P limitation that could lead to a high catabolic activity with a potential increase in the use of SOC by microbial communities in the search for P, thus affecting soil C sequestration, soil quality and the provision of soil-related ecosystem services.

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.

The role of land-use history in driving successional pathways and its implications for the restoration of tropical forests

Secondary forests are increasingly important components of human‐modified landscapes in the tropics. Successional pathways, however, can vary enormously across and within landscapes, with divergent regrowth rates, vegetation structure and species composition. While climatic and edaphic conditions drive variations across regions, land‐use history plays a central role in driving alternative successional pathways within human‐modified landscapes. How land use affects succession depends on its intensity, spatial extent, frequency, duration and management practices, and is mediated by a complex combination of mechanisms acting on different ecosystem components and at different spatial and temporal scales. We review the literature aiming to provide a comprehensive understanding of the mechanisms underlying the long‐lasting effects of land use on tropical forest succession and to discuss its implications for forest restoration. We organize it following a framework based on the hierarchical model of succession and ecological filtering theory. This review shows that our knowledge is mostly derived from studies in Neotropical forests regenerating after abandonment of shifting cultivation or pasture systems. Vegetation is the ecological component assessed most often. Little is known regarding how the recovery of belowground processes and microbiota communities is affected by previous land‐use history. In published studies, land‐use history has been mostly characterized by type, without discrimination of intensity, extent, duration or frequency. We compile and discuss the metrics used to describe land‐use history, aiming to facilitate future studies. The literature shows that (i) species availability to succession is affected by transformations in the landscape that affect dispersal, and by management practices and seed predation, which affect the composition and diversity of propagules on site. Once a species successfully reaches an abandoned field, its establishment and performance are dependent on resistance to management practices, tolerance to (modified) soil conditions, herbivory, competition with weeds and invasive species, and facilitation by remnant trees. (ii) Structural and compositional divergences at early stages of succession remain for decades, suggesting that early communities play an important role in governing further ecosystem functioning and processes during succession. Management interventions at early stages could help enhance recovery rates and manipulate successional pathways. (iii) The combination of local and landscape conditions defines the limitations to succession and therefore the potential for natural regeneration to restore ecosystem properties effectively. The knowledge summarized here could enable the identification of conditions in which natural regeneration could efficiently promote forest restoration, and where specific management practices are required to foster succession. Finally, characterization of the landscape context and previous land‐use history is essential to understand the limitations to succession and therefore to define cost‐effective restoration strategies. Advancing knowledge on these two aspects is key for finding generalizable relations that will increase the predictability of succession and the efficiency of forest restoration under different landscape contexts.

Different responses of soil bacterial and fungal communities to nitrogen deposition in a subtropical forest

China has experienced a widespread increase in N deposition due to intensive anthropogenic activities, particularly in the subtropical regions. However, the effects of long-term N deposition on soil bacterial and fungal abundance, diversity, and community composition remain largely unclear. We assessed the effects of N deposition on soil microbial communities in summer and winter, using quantitative polymerase chain reaction and Illumina Miseq sequencing of bacterial 16S rRNA and fungal ITS genes from subtropical natural forest soils. The abundance of both soil bacteria and fungi exhibited a decreasing pattern with increasing N deposition rates. Nitrogen deposition increased bacterial diversity in both summer and winter, whereas fungal diversity was significantly decreased in summer, but greatly increased under the highest level of N deposition (150 kg N ha^-1 yr^-1) in winter. Nitrogen deposition significantly increased the relative abundance of bacterial phyla Actinobacteria, Chloroflexi, and WPS-2, but decreased that of Acidobacteria and Verrucomicrobia. In addition, N deposition significantly decreased the relative abundance of Ascomycetes, but did not exert any significant effect on Basidiomycetes. The bacterial and fungal community compositions were greatly influenced by N deposition, with soil N availability and soil pH identified as the two most influential soil properties. This study demonstrates that the fungal community was more sensitive than the bacterial community to N deposition, and further emphasizes the importance of simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

Rhizosphere effects on soil microbial community structure and enzyme activity in a successional subtropical forest

Forest succession is a central ecological topic due to the importance of its dynamic process for terrestrial ecosystems. However, we have limited knowledge of the relationship between forest succession and belowground microbiota, particularly regarding interactions in the rhizosphere. Here, we determined microbial community structure and biomass using phospholipid fatty acid (PLFA) biomarkers and microbial activity using extracellular enzyme activity in bulk and rhizosphere soils from three successional stages of subtropical forests in eastern China. Principal component analysis of PLFAs indicated distinct soil microbial communities among different successional stages and habitat locations. Specifically for the topsoil, we found the total microbial biomass, bacterial biomass and enzyme activities showed higher levels in the late than early stage, with a significant succession-induced accentuated rhizosphere effect. The increase in total microbial biomass and activity coincided with a net growth in bacterial rather than fungal biomass, indicating a model in which microbial biomass carrying capacity and activity could be affected by the creation or expansion of niches for certain functional group rather than by a rebalancing of competitive interactions among these groups. Furthermore, we demonstrated that forest succession significantly influenced enzyme activity via the changes in microbial biomass, as driven by edaphic factors. Overall, our study deepens the mechanistic understanding of forest recovery by linking soil microbial community and activity along successional chronosequences.

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale

Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.

The relative importance of spatial and temporal variability in shaping the distribution of soil microbial communities at a large spatial scale remains poorly understood. Here, we explored the relative importance of space versus time when predicting the distribution of soil bacterial and fungal communities across North China Plain in two contrasting seasons (summer versus winter). Although we found that microbial alpha (number of phylotypes) and beta (changes in community composition) diversities differed significantly between summer and winter, space rather than season explained more of the spatiotemporal variation of soil microbial alpha and beta diversities. Environmental covariates explained some of microbial spatiotemporal variation observed, with fast-changing environmental covariates—climate variables, soil moisture, and available nutrient—likely being the main factors that drove the seasonal variation found in bacterial and fungal beta diversities. Using random forest modeling, we further identified a group of microbial exact sequence variants (ESVs) as indicators of summer and winter seasons and for which relative abundance was associated with fast-changing environmental variables (e.g., soil moisture and dissolved organic nitrogen). Together, our empirical field study’s results suggest soil microbial seasonal variation could arise from the changes of fast-changing environmental variables, thus providing integral support to the large emerging body of snapshot studies related to microbial biogeography.

IMPORTANCE Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.

Crop-litter type determines the structure and function of litter-decomposing microbial communities under acid rain conditions

Acid rain has been one of the major environmental problems in industrial countries. While it may affect the litter decomposition, a highly important microbial-driven biogeochemical process, knowledge about the impact of acid rain on litter-decomposing microbial communities and their functions remains unclear. Therefore, this experiment was conducted to investigate how acid rain treatments would alter microbial communities and their functions during litter decomposition of three major commodity crops (maize, rice, and soybean) for six months from June to December 2018. We used litterbag method to determine litter decomposition,while the phospholipid fatty acid (PLFA) and fluorometric methods were used to reveal changes in the litter-adhering microbial community parameters and activities of enzymes involved in the litter decomposition and nutrient release (including carbon [C], nitrogen [N], and phosphorus [P]), respectively. Our results showed that microbial community composition and functions were significantly different among litter types, but not significantly altered by acid rain treatments during the experimental period. The enzyme activities significantly correlated with each other, thus suggesting that microbial requirements for C, N, and P were coupled together during litter decomposition. Moreover, the enzyme activities, at large, did not correlate to microbial community composition, thus indicating the asymmetric relationship between microbial community structure and functions. Our results imply that crop litter type and substrate availability determined the microbial community composition and functions, while litter-inhabiting microbial communities demonstrated substantial resilience under acid rain pressure throughout the experimental period. These results also predict that litter (crop residues) decomposition may not be altered by acid rains in the subtropical agroecosystem, due to relatively high resilience of litter-decomposing microbial communities.

Changes in Soil Microbial Biomass, Community Composition, and Enzyme Activities After Half-Century Forest Restoration in Degraded Tropical Lands

Soil carbon (C) sequestration and stabilization are determined by not only the C input to the soil but also the decomposition rate of soil organic matter (SOM), which is mainly mediated by soil microbes. Afforestation, an effective practice to restore forests from degraded or bare lands, may alter soil microbial properties, and thus soil C and nitrogen (N) dynamics. The aim of this study was to investigate the impacts of different afforestation strategies on soil microbial compositions and activities after afforestation for half a century. Soil samples were collected from two afforested sites (i.e., a restored secondary forest (RSF) and a managed Eucalyptus forest (MEP)) and two reference sites (i.e., a nearby undisturbed forest (UF), representing the climax vegetation and a bare land (BL), representing the original state before restoration) in south China. We quantified the soil microbial biomass, microbial community compositions, and activities of nine extracellular enzymes at different soil depths and in different seasons. Results showed that the soil microbial biomass, all the main soil microbial groups, and the activities of all extracellular enzymes were significantly increased after afforestation compared to the BL sites, while the ratios of fungi/bacteria (F/B), specific enzyme activities, and the ecoenzymatic stoichiometry were significantly decreased regardless of the season and soil depth. Between the two afforested sites, these microbial properties were generally higher in the RSF than MEP. However, the microbial properties in the RSF were still lower than those in the UF, although the differences varied with different seasons, soil depths, and microbial groups or enzymes. Our findings demonstrated that afforestation might significantly improve microbial properties. Afforestation is more effective in mixed-species plantation than in the monoculture Eucalyptus plantation but needs a much longer time to approach an equivalent level to the primary forests.

Spatial patterns in soil physicochemical and microbiological properties in a grassland adjacent to a newly built lake

Soil water content (SWC) is an important determinant for nutrient cycling and microorganism activity in the grassland ecosystem. Lakes have a positive effect on the water supply of the neighboring ecosystem. However, information evaluating whether newly built lakes improve the physiochemical properties and microorganism activity of adjacent grassland soil is rare. A 15‐hectare artificial lake with a 2 m depth was built on grazed grassland to determine whether the change of soil physiochemical properties and microorganism activity of the adjacent grassland depended on the distance from the lake. SWC and total nitrogen (TN) were greater within 150 m of the lake than at distances over 150 m from the lake. The total organic carbon (TOC) increased first at 100–150 m from the lake and then decreased. The soil microbial biomass and the bacterial and fungal contents increased with increasing years after the construction of the lake. Gram‐negative bacteria and methanotrophic bacteria were greater within a 30 m distance of the lake. Over 60 m away from the lake, Actinobacteria, gram‐positive bacteria, and anaerobic bacteria showed higher abundances. In the area near the lake (<250 m distance), microorganisms were strongly correlated with SWC, EC, TN, and TOC and greatly correlated with the changes of total phosphorous (TP) and pH when the distance from the lake was over 250 m. The results indicated that the newly built lake could be a driving factor for improving the physiochemical properties and microorganism activity of adjacent grassland soil within a certain range.

Effect of Different Fertilization Practices on Soil Microbial Community in a Wheat–Maize Rotation System

Little information is known about the effects of different fertilization practices on soil microbiome in intensively managed crop rotations. The objective of this research was to investigate the response of microbial community composition (phospholipid fatty acid, PLFA) and extracellular enzyme activity to fertilization treatments through a three-year experiment. Treatments were: Control (without fertilizer, CK), chemical fertilizer (NPK), NPK + pig manure (NPKM), NPK + straw (NPKS), and NPK + both manure and straw (NPKMS). We found that fertilization had no effect on the microbial abundance except arbuscular mycorrhizal fungi (AMF) PLFA. Soil microbial community composition was significantly affected by crop species and to a lesser extent by fertilization, with a greater influence on the wheat harvest. In addition, soil enzyme activities were enhanced by fertilization, especially in wheat season. Over three years, compared with NPK treatment, addition of organic manure or straw (NPKS and NPKMS) significantly increased the activities of the enzymes except invertase and urease, and the effect was greater at wheat harvest than the maize harvest. Our results indicate that the response of soil microbial community structure and enzyme activities to fertilization takes precedence than microbial biomass in the short term. The temporal variation in soil microbial community structure and enzyme activities in the crop rotation indicate that crop species may be carefully considered for sustainable agricultural intensification management.

Prolonging Rotation of Chinese Fir to over 25 Years Could Maintain a Better Soil Status in Subtropical China

Although Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important species for wood production in subtropical China, it serious declines in soil nutrients and timber productivity in plantations have been reported, probably caused by successive rotation and inappropriate cutting time. Although the significant effect of stand age on soil properties has been widely recognized, research on soil enzymes and microbial communities is relatively rare. In this study, assuming that short rotation period is one important reason for soil degradation, we measured soil physicochemical properties, microbial community composition, and enzyme activity in 3-, 15-, 25- and 45-year Chinese fir forests in Jiangxi province of China. Soil organic carbon (SOC) content decreased from 3-year to 25-year stands and then increased in 45-year stands. Despite the significant relationship between SOC and the abundance of total phospholipid fatty acids (PLFAs), no notable changes in the abundance of PLFAs were detected with increasing tree ages, except for the abundances of arbuscular mycorrhizal fungi (AMF) which were significantly higher in 25-year stands. However, the ratios of gram-positive to gram-negative bacteria (G+/G−) and fungi to bacteria (F/B) both decreased with increasing stand age. 45-year stands showed the highest activities of both phosphatase and β-glucosidase. Total potassium (TK) content and net N mineralization rate both had significant links with soil microbial community structure. Collectively, our study emphasized that stand age could significantly affect soil physicochemical properties and the microbial community. In general, 25-year stands showed poorer soil status compared to that of 45-year stands. Thus, the cutting age of Chinese fir should be increased to over 25 years to maintain a better soil status.

Soil Microbial Biomass and Fungi Reduced With Canola Introduced Into Long-Term Monoculture Wheat Rotations

With increasing canola (Brassica napus L.) acreage in the Inland Pacific Northwest of the USA, we investigated the effect of this relatively new rotational crop on soil microbial communities and the performance of subsequent wheat (Triticum aestivum L.) crops. In a 6-year on-farm canola-wheat rotation study conducted near Davenport, WA, grain yields of spring wheat (SW) following winter canola (WC) were reduced an average of 17% compared to SW yields following winter wheat (WW). Using soil samples collected and analyzed every year from that study, the objective of this research was to determine the differences and similarities in the soil microbial communities associated with WC and WW, and if those differences were associated with SW yield response. Microbial biomass and community composition were determined using phospholipid fatty acid analysis (PLFA). The WC-associated microbial community contained significantly less fungi, mycorrhizae, and total microbial biomass than WW. Additionally, reduced fungal and mycorrhizal abundance in SW following WC suggests that the canola rotation effect can persist. A biocidal secondary metabolite of canola, isothiocyanate, may be a potential mechanism mediating the decline in soil microbial biomass. These results demonstrate the relationship between soil microbial community composition and crop productivity. Our data suggest that WC can have significant effects on soil microbial communities that ultimately drive microbially mediated soil processes.

Dynamics of oxytetracycline and resistance genes in soil under long-term intensive compost fertilization in Northern China

In the present study, we explored the dynamics of antibiotics (ciprofloxacin, norfloxacin, enrofloxacin, and oxytetracycline), tetracycline resistance genes (TRGs), and bacterial communities over 2013-2015 in soils fertilized conventionally or with two levels (82.5 and 165 t/ha) of compost for 12 years. In the soil receiving 165 t/ha of compost, only oxytetracycline was 46% higher than that in the conventionally fertilized soil. Transient enrichment of both tetM (20% to 9-fold) and tetK (25% to 67-fold) was observed in multiple instances immediately after the application of compost. The majority of genera which positively correlated with tetM or tetK were affiliated to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The structural equation model analysis indicated that fertilization regimes directly affected the bacterial composition and antibiotics and had an indirect effect on the abundance of tetK and tetM via these antibiotics. In summary, this study shed light into the complex interactions between fertilization, antibiotics, and antibiotic resistance pollution in greenhouse soil.

Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents

Evergreen broad-leaved (EBF) and deciduous broad-leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.

Changes in Fungal Communities across a Forest Disturbance Gradient

Deforestation has a substantial impact on aboveground biodiversity, but the response of belowground soil fungi remains poorly understood. In a tropical montane rainforest in southwestern China, plots were established along a forest degradation gradient ranging from mature and regenerated forests to open land to examine the impacts of forest degradation and deforestation on ecosystem diversity and function. Here, we evaluated the changes in belowground fungal diversity and community composition using a metabarcoding approach. Soil saprotrophic fungal richness declined with increasing forest disturbance. For example, Penicillium spp. (phosphorus [P]-solubilizing fungi) dominated in mature forest but were less abundant in regenerating forests and showed the lowest abundance in open land sites. Conversely, the abundance of facultative pathogenic fungi increased along the disturbance gradient. The decline in soil saprophytic fungi may be a direct result of forest disturbance or it may be associated with increased availability of soil phosphorus indirectly through an increase in soil pH. The increase in abundance of facultative pathogenic fungi may be related to reduced competition with saprotrophic fungi, changes in microclimate, or increased spore rain. These results demonstrate a loss of dominant P-solubilizing saprotrophic fungi along the disturbance gradient, indicating a change from soil P limitation in mature tropical forests to soil C limitation in deforested sites. The increased prevalence of pathogenic fungi may inhibit plant succession following deforestation. Overall, this research demonstrates that soil fungi can be used as a sensitive indicator for soil health to evaluate the consequences of forest disturbance.IMPORTANCE The soil fungal functional group changes in response to forest disturbance and indicates a close interaction between the aboveground plant community and the belowground soil biological community. Soil saprotrophic fungi declined in relative abundance with increasing forest disturbance. At the same time, the relative abundance of facultative pathogenic fungi increased. The loss of saprotrophic fungal richness and abundance may have been a direct result of forest disturbance or an indirect result of changes in soil pH and soil P. Furthermore, the dominant P-solubilizing saprotrophic fungi were replaced by diverse facultative pathogenic fungi, which have weaker C decomposition ability. These changes potentially indicate a shift from soil phosphate limitation to carbon limitation following deforestation. This study suggests that changes in fungal functional group composition can be used as an indicator of the effects of forest disturbance on soil carbon and nutrients.

Diurnal Temperature Variation and Plants Drive Latitudinal Patterns in Seasonal Dynamics of Soil Microbial Community

Seasonality, an exogenous driver, motivates the biological and ecological temporal dynamics of animal and plant communities. Underexplored microbial temporal endogenous dynamics hinders the prediction of microbial response to climate change. To elucidate temporal dynamics of microbial communities, temporal turnover rates, phylogenetic relatedness, and species interactions were integrated to compare those of a series of forest ecosystems along latitudinal gradients. The seasonal turnover rhythm of microbial communities, estimated by the slope (w value) of similarity-time decay relationship, was spatially structured across the latitudinal gradient, which may be caused by a mixture of both diurnal temperature variation and seasonal patterns of plants. Statistical analyses revealed that diurnal temperature variation instead of average temperature imposed a positive and considerable effect alone and also jointly with plants. Due to higher diurnal temperature variation with more climatic niches, microbial communities might evolutionarily adapt into more dispersed phylogenetic assembly based on the standardized effect size of MNTD metric, and ecologically form higher community resistance and resiliency with stronger network interactions among species. Archaea and the bacterial groups of Chloroflexi, Alphaproteobacteria, and Deltaproteobacteria were sensitive to diurnal temperature variation with greater turnover rates at higher latitudes, indicating that greater diurnal temperature fluctuation imposes stronger selective pressure on thermal specialists, because bacteria and archaea, single-celled organisms, have extreme short generation period compared to animal and plant. Our findings thus illustrate that the dynamics of microbial community and species interactions are crucial to assess ecosystem stability to climate variations in an increased climatic variability era.

New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering

Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.

Contrasting Effects of Chinese Fir Plantations of Different Stand Ages on Soil Enzyme Activities and Microbial Communities

Soil enzymes and microbial communities are key factors in forest soil ecosystem functions and are affected by stand age. In this study, we studied soil enzyme activities, composition and diversity of bacterial and fungal communities and relevant physicochemical properties at 0–10 cm depth (D1), 10–20 cm depth (D2) and 20–30 cm depth (D3) soil layers in 3-(3a), 6-(6a), 12-(12a), 18-(18a), 25-(25a), 32-(32a) and 49-year-old (49a) Chinese fir plantations to further reveal the effects of stand age on soil biotic properties. Spectrophotometry and high-throughput sequencing was used to assess the soil enzyme activity and microbial community composition and diversity of Chinese fir plantation of different stand ages, respectively. We found that soil catalase activity increased as the stand age of Chinese fir plantations increased, whereas the activities of urease, sucrase and β-glucosidase in 12a, 18a and 25a were lower than those in 6a, 32a and 49a. Shannon and Chao1 indices of bacterial and fungal communities first decreased gradually from 6a to 18a or 25a and then increased gradually from 25a to 49a. Interestingly, the sucrase and β-glucosidase activities and the Shannon and Chao1 indices in 3a were all lower than 6a. We found that the relative abundance of dominant microbial phyla differed among stand ages and soil depths. The proportion of Acidobacteria first increased and then decreased from low forest age to high forest age, and its relative abundance in 12a, 18a and 25a were higher than 3a, 32a and 49a, but the proportion of Proteobacteria was opposite. The proportion of Ascomycota first decreased and then increased from 6a to 49a, and its relative abundance in 12a, 18a and 25a was lower than 3a, 6a, 32a and 49a. Our results indicate that soil enzyme activities and the richness and diversity of the microbial community are limited in the middle stand age (from 12a to 25a), which is important for developing forest management strategies to mitigate the impacts of degradation of soil biological activities.

Variations in Soil Bacterial Community Diversity and Structures Among Different Revegetation Types in the Baishilazi Nature Reserve

We compared patterns of soil bacterial community diversity and structure in six secondary forests (JM, Juglans mandshurica; QM, Quercus mongolica; MB, mixed Broadleaf forest; BE, Betula ermanii; CB, conifer-broadleaf forest; PT, Pinus tabuliformis) and two plantation forests (LG, Larix gmelinii; PK, Pinus koraiensis) of the Baishilazi Nature Reserve, China, based on the 16S rRNA high-throughput Illumina sequencing data. The correlations between the bacterial community and soil environmental factors were also examined. The results showed that the broadleaf forests (JM, QM, MB) had higher levels of total C (TC), total N (TN), available N (AN), and available K (AK) compared to the coniferous forests (PT, LG, PK) and conifer-broadleaf forest (CB). Different revegetation pathways had different effects on the soil bacterial community diversity and structure. For the α-diversity, the highest Shannon index and Simpson index were found in JM. The Simpson index was significantly positively correlated with the available P (AP) (P < 0.05), and the Shannon index was significantly positively correlated with AK (P < 0.05). Compared with others, the increased ACE index and Chao1 index were observed in the CB and MB, and both of these α-diversity were significantly negative with AK (P < 0.05). The relative abundances of bacterial phyla and genera differed among different revegetation types. At the phylum level, the dominant phylum groups in all soils were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, Chloroflexi, Bacteroidetes, Gemmatimonadetes, and Planctomycetes. Significant differences in relative abundance of bacteria phyla were found for Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Proteobacteria. Correlation analysis showed that Soil pH, TC, TN, AP, and AK were the main abiotic factors structuring the bacterial communities. As revealed by the clear differentiation of bacterial communities and the clustering in the heatmap and in the PCA plots, broadleaf forests and coniferous forests harbored distinct bacterial communities, indicating a significant impact of the respective reforestation pathway on soil bacterial communities in the Baishilazi Nature Reserve.

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems.

Changes in soil microbial community structure and function after afforestation depend on species and age: Case study in a subtropical alluvial island

It is well established that land use change can have a profound impact on soil physicochemical properties but the associated changes in soil microbial communities are poorly understood. We used long-term research sites in a subtropical alluvial island of eastern China to measure changes in soil physicochemical properties and microbial community abundance and composition (via phospholipid fatty acid (PLFA) analysis) and function (via extracellular enzyme activity) across different land use types developed on the same soil matrix, including a camphor (Cinnamomum camphora) plantation, a chronosequence of differently aged dawn redwood (Metasequoia glyptostroboides) plantings, a deforested land and a rice paddy. We hypothesized that afforestation could improve soil quality by enhancing carbon (C) and nitrogen (N) contents, microbial biomass and enzyme activities, but that this effect would vary depending on forest age and tree species. Soil C and N concentrations, PLFA abundances and activities of decomposition enzymes (β-glucosidase, urease, alkaline phosphatase and catalase) in older plantations all increased significantly compared to cropland. These variables changed little or decreased in deforested land compared to cropland. These variables also increased with planting age in the dawn redwood plantings. Soils under camphor plantations had higher soil nutrient contents, microbial biomass and lower enzyme activities than dawn redwood soils with similar age. We also found some significant relationships between soil chemical and biological properties: PLFA abundances were positively related to soil organic matter (SOM) contents; the fungal-to-bacterial ratio and fungal relative abundance were correlated positively with SOM contents and negatively with C/N ratio; both soil PLFA abundances and enzyme activities were positively linked with soil inorganic N content and potential net N mineralization rate; ratio of specific C, N and P (phosphorus) acquisition activities was limited to 10: 1: 10 across land use types. Our study underscores the fact that land use type can have a profound impact on soil microbial communities; in addition, tree species and planting age also play significant roles in afforestation.