Soil Microbial Ecology
Publication years
Loading ...
Article types
Loading ...
  • Select all
    Qi Shao, Xuejing Xia, Guihua Li, Hui Li, Jitong Lin, Yanhong Lou, Quangang Yang, Hui Wang, Zhongchen Yang, Hong Pan, Yuping Zhuge
    Soil Ecology Letters, 2024, 6(1): 230185.

    ● Flue gas desulfurization gypsum and clover planting alleviated the soil salinization stress.

    ● Soil pH and total phosphorus affected the bacterial communities.

    ● Total phosphorus affected the fungal communities.

    ● Flue gas desulfurization gypsum and clover planting improved jujube quality.

    The coastal area of Shandong Province, characterized by coastal saline tidal soil, is one of the main production areas of winter jujube in China. However, the low soil fertility and poor soil structure in jujube orchard restricted the development of the jujube industry. The objectives of this study were to 1) evaluate the effect of application of flue gas desulfurization (FGD) gypsum and clover planting on soil quality improvement and soil microbial community structure of jujube orchard; 2) investigate the effects of two measures on the nutrition and quality of winter jujube. The results showed that FGD gypsum reduced the soil total salt content by 65.6%, and clover planting increased the soil organic matter content by 30.7%, which effectively alleviated the soil salinization stress and improved the soil structure. Soil pH and total phosphorus (TP) were the main determinants influencing bacterial community composition, and TP was the dominant factor of the fungal community composition in the saline-alkali soils. Meanwhile, FGD gypsum addition and clover planting significantly increased the sugar degree and Vc content of winter jujube, thus improved jujube quality, and further contributed to the ecological sustainable development of winter jujube industry.

    Matheus Emannuel Oliveira Vieira, Lucas Dantas Lopes, France Mário Costa, Viviane Talamini, Edson Patto Pacheco, Marcelo Ferreira Fernandes
    Soil Ecology Letters, 2024, 6(1): 230191.

    ● Integrated grain cropping systems promote soil health (SH) and sustainability.

    ● Microbial biomass and activity (MBA) and community structure (MCS) are key to SH.

    ● Integration of maize with Urochloa pastures strongly impacts MBA and MCS.

    ● MBA is more sensitive than MCS to shifts in grain cropping systems.

    ● Systems under continuous Urochloa increased microbial activity and AMF abundance.

    Tropical soils are prone to degradation. Adoption of conservation agricultural practices is essential to improve soil health, which is influenced by soil microbes. In this study we analyzed shifts in microbial biomass and activity (MBA) and microbial community structure (MCS) based on fatty acid methyl esthers (FAMEs) between five no-till agricultural practices: maize monoculture (MM); maize annualy intercropped with Urochloa decumbens (M/Ud); M/Ud with soybean rotation every other year (M/Ud–S); M/Ud keeping the pasture for the next two years (M/Ud–Ud–Ud); and maize intercropped with U. ruziziensis keeping the pasture for the next two years (M/Ur–Ur–Ur). Results indicated that MBA was affected by the inclusion of Urochloa intercropping and by rotation with soybean. Systems under a longer residence time with Urochloa in the field had higher β-glucosidase activity and soil basal respiration, indicating a greater microbial activity. MCS was less affected than MBA by the investigated cropping systems. MCS changed only in the continuous pasture systems, which were enriched in arbuscular mycorrhyzal fungi (AMF). Additionally, the continuous pasture systems had lower microbial stress ratios than the other agricultural practices. In sum, our study showed that utilization of Urochloa spp. under longer periods in no-till agricultural practices contributes to increase microbial activity, AMF abundance and decrease microbial stress ratio. These changes are primarily beneficial for soil health.

    Thomas Pommier
    Soil Ecology Letters, 2023, 5(4): 230180.
    Wenfei Liao, Di Tong, Xiaodong Nie, Yaojun Liu, Fengwei Ran, Shanshan Liao, Jia Chen, Aoqi Zeng, Zhongwu Li
    Soil Ecology Letters, 2023, 5(4): 230173.

    ● Soil erosion resulted in homogenization of bacterial communities in the watershed.

    ● Microbial community heterogeneity among erosion sites made soil tracing possible.

    ● Assembly process results showed that the tracking results can achieve high precision.

    ● Dryland was the main source of sediment deposition based on the result of FEAST.

    Sediment source tracing can accurately provide a theoretical basis for controlling soil erosion effectively, by identifying the most serious types of land use. Traditional sediment tracing methods are based on physical, chemical, biological, and composite fingerprinting, which have not included microbes. As high-throughput sequencing becomes more prevalent, microorganisms can provide more information than what we think. Thus, whether the microorganism can also be used as a special fingerprint factor for sediment source identification during soil erosion, we have tested it by using microbial source tracking tool FEAST to quantify the microbe contribution from five types of eroded land (including dryland, urban, paddy field, forest and grassland) to the depositional areas (Niubitan) in the Yuanjiang basin. The source microbial community in the erosive area was heterogeneous, and assembly process analysis further demonstrated that the source tracking results could reach higher accuracy. The results of FEAST showed that dryland (35.50%), urban (17.21%), paddy field (8.14%), and forest (1.07%) were the major contributors to Niubitan. Our results follow the general soil erosion rules and prove its validity. Taken together, a new perspective is provided by these results for tracing sediment sources in erosion-sedimentary systems.

    George P. Stamou, Nikolaos Monokrousos, Anastasia Papapostolou, Effimia M. Papatheodorou
    Soil Ecology Letters, 2023, 5(3): 220161.

    ● We assess the recovery of microbial networks underneath crust to repeated rainfall.

    ● The network fragmentation after the second heavy rain was milder than at the first one.

    ● Cohesive networks were related to high enzyme activity involved in C, N, and P cycles.

    ● Loose networks were related to high Ca, K, Mg, NH4 and organic N.

    ● The network in dry-crusted soils collapsed after the second heavy rain.

    Biological soil crusts (BSCs) are an important multi-trophic component of arid ecosystems in the Mediterranean region. In a mesocosm experiment, the authors investigated how the network of interactions among the members of the soil microbial communities in four types of soil sample responded when soils were exposed to two simulated extreme rain events. The four types of soil samples were: covered by Cladonia rangiformis and previously hydrated (+BSC+H), covered by C. rangiformis and dried (+BSC-H), uncovered and hydrated (-BSC+H), uncovered and dried (-BSC-H). Network analysis was based on the co-occurrence patterns of microbes; microbes were assessed by the phospholipid fatty acids analysis. The authors further explored the relations between networks’ metrics and soil functions denoted by enzymatic activity and soil chemical variables. All networks exhibited Small world properties, moderate values of clustering coefficient and eigen centrality, indicating the lack of hub nodes. The networks in -BSC-H soils appeared coherent during the pre-rain phases and they became modular after rains, while those in +BSC-H soils kept their connectivity till the second rain but this then collapsed. The network metrics that were indicative of cohesive networks tended to be related to enzyme activity while those that characterized the loose networks were related to Ca, K, Mg, NH4+ and organic N. In all mesocosms except for +BSC-H, networks’ fragmentation after the second heavy rain was milder than after the first one, supporting the idea of community acclimatization. The response of microbial networks to heavy rains was characterized by the tendency to exhibit degradation-reconstruction phases. The network collapse in the crusted only mesocosms showed that the communities beneath crusts in arid areas were extremely vulnerable to recurring heavy rain events.

    Gaidi Ren, Guangfei Wang, Dejie Guo, Chao Lu, Yan Ma
    Soil Ecology Letters, 2023, 5(1): 46-65.

    • Sugar addition caused vigorous proliferation of wilt pathogen.

    • Sugar addition modified bacterial community structure and decreased the diversity.

    • Sugar addition caused more complex and connected networks.

    • Keystone taxa formed positive links with wilt pathogen in sugar-spiked networks.

    Sugars are frequently and abundantly found in root exudates, but influence of specific sugars on the fate of soil-borne pathogens, microbiome structure, and particularly microbial interactions are not well understood. A 42-day of microcosm incubation was conducted with two soils: a natural watermelon Fusarium wilt pathogen (i.e., Fusarium oxysporum f. sp. niveum (FON))-infested soil (Low-FON soil) and the soil further receiving the wilt pathogen inocula (High-FON soil). Both soils were supplemented with four simple sugars before incubation. The results show that, in both soils, FON was enriched by all sugars although co-living with tremendously diverse microbes; and bacterial richness, evenness, and diversity were decreased and bacterial community structure was changed by all sugars. Bacterial richness and evenness were negatively correlated with FON quantity in both Low-FON and High-FON soils, indicating that FON may tend to live in soil with low alpha-diversity. In both Low-FON and High-FON soils, the sugar-spiked networks had more links, higher density, larger modules, and shorter harmonic geodesic distance, suggesting greater potentials for microbial interaction and niche-sharing. The positive links between some of the keystone taxa and FON indicates that these keystone taxa may have promoted FON. This may be one of reasons why FON could proliferate vigorously after sugar supplementation.

    Xiaojing Hu, Haidong Gu, Junjie Liu, Baoku Zhou, Dan Wei, Xueli Chen, Guanghua Wang
    Soil Ecology Letters, 2022, 4(4): 348-361.

    • Fungal communities were more sensitive to N fertilizers than P, K fertilizers.

    • More harmonious and stable fungal network induced by P, K fertilizers.

    • N fertilizers induced lower fungal community resistance with detriments on crop yields.

    Nitrogen (N), phosphate (P), and potassium (K) are the three most important nutrients applied into agricultural soils, but the impacts of their single or combined application on soil fungal community structure and stability are still open questions. Using qPCR and Illumina Miseq sequencing, the variation of soil fungal communities in response to long-term addition of N, P, or K fertilization alone and their combinations in a Mollisol field was investigated in this study. In addition, the fungal community resistance indices and network structure were studied. Results showed that N fertilizations (N, NK, NP and NPK treatments) rather than P, K fertilizations (P, K and PK treatments) significantly increased fungal abundance, but decreased fungal diversity and shifted fungal community structures when compared to non-fertilization (NoF). Additionally, N fertilization treatments presented lower resistance of fungal communities to environment disturbances than those of P, K fertilization treatments. More numbers and higher abundances of changed fungal taxa at the genus and OTU levels were induced by N fertilizations rather than by addition of P, K fertilizers. In addition, N fertilizations induced a more changeable fungal network and complex pathogenic subnetwork with many positive interactions among responding plant pathogens (RP, the changeable plant pathogens induced by fertilizers addition compared to NoF) when compared to P, K fertilizations. These RP directly and negatively influenced fungal community resistance examined by structural equation modeling (SEM), which were indirectly detrimental to soybean yields. Our findings revealed that addition of N fertilizers significantly disturbed fungal communities and promoted pathogenic interactions, and provided insights into the optimization of fertilization strategies toward agricultural sustainability.

    Haojie Feng, Hong Pan, Chengliang Li, Yuping Zhuge
    Soil Ecology Letters, 2022, 4(4): 337-347.

    • Both organic and inorganic fertilizations stimulate soil aggregation.

    • Organic and inorganic fertilizers enhance organic carbon storage at aggregate scale.

    • Aggregate-associated bacterial communities were more sensitive to organic fertilizers than to chemical ones.

    • The complexity of bacterial network structures decreased with decreasing of aggregate size.

    • The competitive interactions among bacterial communities were intensified with decreasing of aggregate size.

    Differently sized soil aggregates, with non-uniform distribution of space and nutrients, provide spatially heterogeneous microenvironments for microorganisms and are important for controlling microbial community ecology and biogeochemistry in soils. Here, we investigated the prokaryotic communities within different aggregate-size fractions: macroaggregate (>0.25 mm), microaggregate (0.053–0.25 mm) and silt+ clay (<0.053 mm). These were isolated from fluvo-aquic soils under 39-year fertilization strategies: no fertilizer (CK), chemical fertilizer (NPK), manure fertilizer (M), and combination of manure and chemical fertilizers (MNPK). The results showed that the proportion of macroaggregate, soil aggregate-associated organic carbon (SOC) content and aggregate stability were all significantly increased by both manure and chemical fertilizations. Organic fertilizations (M and MNPK) more effectively boosted formation and stability of macroaggregates and enhanced SOC concentration than NPK. The distribution patterns of microorganisms in aggregates were primarily shaped by fertilization and aggregate size. They explained 76.9% of the variance in bacterial community compositions. Fertilizations, especially with organic fertilizers primarily transitioned bacterial communities from slow-growing oligotrophic groups (e.g., Chloroflexi) dominance to fast-growing copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) dominance across all aggregate sizes. Macroaggregates possessed a more stable bacterial community and efficiency of resource transfer, while smaller aggregates increased antagonism and weakened mutualism among bacterial communities. Overall, combination of manure and chemical fertilizers was crucial for increasing SOC content and aggregation, leading to a clear shift in bacterial community structures at aggregate scale.

    Yitian Yu, Qi Zhang, Zhenyan Zhang, Nuohan Xu, Yan Li, Mingkang Jin, Guoqiang Feng, Haifeng Qian, Tao Lu
    Soil Ecology Letters, 2023, 5(1): 66-78.

    • Continuous chlorine treatment have no obvious effect on soil microbial community structure and composition.

    • Residual chlorine slightly affected soil microbial functions.

    • Daily use of chlorine-containing disinfectants slightly threatened the soil ecosystem.

    Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application of chlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.

    Gaofei Jiang, Ningqi Wang, Yaoyu Zhang, Zhen Wang, Yuling Zhang, Jiabao Yu, Yong Zhang, Zhong Wei, Yangchun Xu, Stefan Geisen, Ville-Petri Friman, Qirong Shen
    Soil Ecology Letters, 2021, 3(4): 356-366.

    • 10-year of CC was a cut-off point in separating soil bacterial community structures.

    • soil pH and P were well associated with changes of diversity and community structures.

    • N fixation bacteria were increased with successive year, but P, K solubilizing bacteria decreased.

    • Monocropped alfalfa simplified the complexity of the cooccurrence networks.

    Soil-borne plant diseases cause major economic losses globally. This is partly because their epidemiology is difficult to predict in agricultural fields, where multiple environmental factors could determine disease outcomes. Here we used a combination of field sampling and direct experimentation to identify key abiotic and biotic soil properties that can predict the occurrence of bacterial wilt caused by pathogenic Ralstonia solanacearum. By analyzing 139 tomato rhizosphere soils samples isolated from six provinces in China, we first show a clear link between soil properties, pathogen density and plant health. Specifically, disease outcomes were positively associated with soil moisture, bacterial abundance and bacterial community composition. Based on soil properties alone, random forest machine learning algorithm could predict disease outcomes correctly in 75% of cases with soil moisture being the most significant predictor. The importance of soil moisture was validated causally in a controlled greenhouse experiment, where the highest disease incidence was observed at 60% of maximum water holding capacity. Together, our results show that local soil properties can predict disease occurrence across a wider agricultural landscape, and that management of soil moisture could potentially offer a straightforward method for reducing crop losses to R. solanacearum

    Lin Xu, Bingchang Zhang, Entao Wang, Bingjian Zhu, Minjie Yao, Chaonan Li, Xiangzhen Li
    Soil Ecology Letters, 2021, 3(4): 328-341.

    • Biocrust succession alters diazotrophic diversity and community compositions.

    • Deterministic processes govern diazotrophic community assemblages.

    • The TOC/TN ratio is a key factor driving diazotrophic community succession.

    • Diazotrophic networks become less complex with biocrust succession.

    The diazotrophic community in biological soil crusts (biocrusts) is the key supplier of nitrogen in dryland. To date, there is still limited information on how biocrust development influences the succession of diazotrophic community, and what are the most important factors mediating diazotrophic communities during biocrust succession. Using the high throughput nifH amplicon sequencing, the diazotrophs in soils at different developmental stages of biocrust were comparatively studied. The results evidenced the decrease of TOC/TN ratio and pH value with biocrust development. Nostoc and Scytonema were the most dominant diazotrophic genera at all biocrust stages, while Azospirillum and Bradyrhizobium were abundant only in bare soil. Diazotrophic co-occurrence networks tended to be less complex and less connected with biocrust succession. The soil TOC/TN ratio was the most dominant factor mediating diazotrophic diversity, community composition and assembly processes, while diazotrophic-diversity and NO3-N/NH4+-N ratio were positively correlated with the nitrogenase activity during biocrust succession. This study provided novel understandings of nitrogen fixation and succession patterns of diazotrophic community, by showing the effects of biocrust succession on diazotrophic diversity, community composition, community assembly and co-occurrence networks, and recognizing TOC/TN ratio as the most dominant factor mediating diazotrophs during biocrust succession.

    Ziheng Peng, Zhifeng Wang, Yu Liu, Tongyao Yang, Weimin Chen, Gehong Wei, Shuo Jiao
    Soil Ecology Letters, 2021, 3(4): 342-355.

    • Soil phosphorus shaped both abundant and rare bacterial communities.

    • ŸBoth abundant and rare bacteria exhibited different assembly strategies with successional reforestation.

    • Deterministic processes increased with succession reforestation.

    Uncovering the mechanisms underlying the diversity patterns of abundant and rare species is crucial for terrestrial biodiversity maintenance. However, the response of abundant and rare community assembly to ecological succession has not been explored, particularly considering soil profiles. Here 300 soil samples were collected from reforestation ecosystems from depths of up to 300 cm and horizontal distances of 30-90 cm from a tree. We revealed that soil phosphorus not only affected alpha diversity and community structure, but also mediated the balance of stochastic and deterministic processes for abundant and rare sub-communities, which exhibited contrasting assembly strategies. The abundant sub-community changed from variable selection to stochasticity with the increase of phosphorus, while the rare sub-community shifted from homogeneous selection to stochasticity. Dispersal limitation was the main assembly process in the abundant sub-community, while the rare sub-community was governed primarily by homogeneous selection. Moreover, the relative influence of deterministic processes increased with succession for both sub-communities. At the scale of a single tree, stochastic processes increased with soil depth in rare sub-community, while deterministic processes increased with the radius from a single tree in the abundant sub-community. Overall, our results highlight the importance of the soil phosphorus-driven assembly process in understanding the re-assembly and maintenance of soil bacterial diversity.

    Jingli Yu, Jingjing Xia, Qiaoli Ma, Chi Zhang, Ji Zhao, Xininigen Tanggood, Yunfeng Yang
    Soil Ecology Letters, 2021, 3(4): 303-312.

    • The riverbed-oxbow lake bed-floodplain-terrace continuum.

    • Dominant bacteria substantially differed along the continuum.

    • The highest bacterial diversity in floodplains and the lowest in terraces.

    • Soil particle and moisture-related factors determine bacterial communities.

    Continuous landscape components along the lateral riverside are affected by both hydrologic connectivity and disconnectivity. In recent years, anthropogenic activities and climate changes have caused wetland shrinkage and land degradation along the lateral riverside of many arid and semiarid regions. Since microorganisms are major drivers of soil biochemical cycling, it is essential to examine soil microbial communities along the lateral landscape continuum to understand their ecosystem functioning and predict future land changes. Here, we collected samples along a lateral riverbed center-riverbed edge-oxbow lake-floodplain-terrace continuum in the Xilin River Basin, Inner Mongolia, China. The floodplain had the highest microbial diversity and heterogeneity, with Bacteroidetes, β- and ©-Proteobacteria being the most abundant taxa. In contrast, the terrace had the lowest microbial diversity and heterogeneity, with Acidobacteria, Actinobacteria, Verrucomicrobia, Gemmatimonadetes, and α-Proteobacteria as the most abundant taxa. Silt particle, salinity, and moisture were the most influential factors for bacterial communities along the riverside continuum. Altogether, we demonstrate that dominant bacterial lineages, soil particles, and moisture-related factors are valuable indicators of this continuum, which can be leveraged for early prediction of drought-induced wetland shrinkage and grassland desertification.

    Peipei Xue, Alex B. McBratney, Budiman Minasny, Tony O'Donnell, Vanessa Pino, Mario Fajardo, Wartini Ng, Neil Wilson, Rosalind Deaker
    Soil Ecology Letters, 2022, 4(1): 57-68.

    • Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils.

    • Bacterial community in topsoils was influenced by both soil orders and soil forms, however, in subsoils it was more impacted by soil orders.

    • Cropping increased the similarity of bacteria structures among different soil orders.

    Human disturbances to soils can lead to dramatic changes in soil physical, chemical, and biological properties. The influence of agricultural activities on the bacterial community over different orders of soil and at depth is still not well understood. We used the concept of genoform and phenoform to investigate the vertical (down to 1 m depth) soil bacterial community structure in paired genosoils (undisturbed forests) and phenosoils (cultivated vineyards) in different soil orders. The study was conducted in the Hunter Valley area, New South Wales, Australia, where samples were collected from 3 different soil orders (Calcarosol, Chromosol, and Kurosol), and each soil order consists of a pair of genosoil and phenosoil. The bacterial community structure was analyzed using high-throughput sequencing of 16S rRNA. Results showed that bacterial-diversity decreased with depth in phenosoils, however, the trend is less obvious in genoform profiles. Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils. Thus, cropping not only affected topsoil bacteria community but also decreased its diversity in the subsoil. Bacterial community in topsoils was influenced by both soil orders and soil forms, however, in subsoils it was more impacted by soil orders. Constrained Analysis of Principal Coordinates revealed that cropping increased the similarity of bacterial structures of different soil orders. This study highlighted the strong influence of agricultural activities on soil microbial distribution with depth, which is controlled by soil orde

    Alin Song, Zimin Li, Yulin Liao, Yongchao Liang, Enzhao Wang, Sai Wang, Xu Li, Jingjing Bi, Zhiyuan Si, Yanhong Lu, Jun Nie, Fenliang Fan
    Soil Ecology Letters, 2021, 3(4): 395-408.

    • Straw returning significantly affects silicon fraction transformation;

    • Straw return affects soil microbial community composition;

    • Soil microbe interacts with silicon fraction transformation and promote rice yield.

    Returning crop straw into the soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for the healthy growth of rice. However, owing to little knowledge about soil microbial communities responsible for straw degradation, how straw return affects Si bioavailability, its uptake, and rice yield remains elusive. Herein, we investigate the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results show that rice straw return significantly increased soil bioavailable Si and rice yield from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, when compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at phylum level, Deltaproteobacteria, and Holophagae at class level was negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide-combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility by altering its transformation, thus resulting in the balance of various nutrient sources to drive biological Si cycle in agroecosystem.

    Ying Chen, Mengguang Han, Xia Yuan, Guangmin Cao, Biao Zhu
    Soil Ecology Letters, 2021, 3(4): 383-394.

    • We measured soil variables along the profile in two alpine ecosystems.

    • Most of soil properties decreased with depth and varied with time.

    • Root and microbial biomass decreased with depth and increased with time.

    • Soil enzyme activities decreased with depth but showed little change with time.

    • Soil properties and microbial biomass were more dynamic than enzyme activities.

    Microbial biomass and extracellular enzyme activities control the rate of soil organic carbon decomposition, thereby affecting soil carbon pool. However, seasonal dynamics of soil microbial properties at different depths of the soil profile remain unclear. In this study, we sampled soils in the early, middle and late growing season at different soil depths (0–100 cm) in two alpine ecosystems (meadow and shrubland) on the Tibetan Plateau. We measured plant belowground biomass, soil properties, microbial biomass and extracellular enzyme activities. We found that soil properties changed significantly with sampling time and soil depth. Specifically, most of soil properties consistently decreased with increasing soil depth, but inconsistently varied with sampling time. Moreover, root biomass and microbial biomass decreased with increasing soil depth and increased with sampling time during the growing season. However, microbial extracellular enzyme activities and their vector properties all changed with depth, but did not vary significantly with time. Taken together, these results show that soil properties, microbial biomass and extracellular enzyme activities mostly decline with increasing depth of the soil profile, and soil properties and microbial biomass are generally more variable during the growing season than extracellular enzyme activities across the soil profile in these alpine ecosystems. Further studies are needed to investigate the changes in soil microbial community composition and function at different soil depths over the growing season, which can enhance our mechanistic understanding of whole-profile soil carbon dynamics of alpine ecosystems under climate change.

    Amit Kumar, Evgenia Blagodaskaya, Michaela A. Dippold, Vicky M. Temperton
    Soil Ecology Letters, 2022, 4(4): 444-453.

    •Intercropping effects on yield advantages are crop species specific.

    •We measured kinetic parameters of three important enzymes in the rhizospheres of individual crop species in both mono and mixed cultures.

    •In moderately nitrogen enriched soils, phosphorus becomes important nutrient element, involved in nutrient facilitation.

    •Positive relative interaction index for faba bean when intercropped with either lupine or maize showed net facilitative interactions.

    Less attention has been given to soil enzymes that contribute to beneficial rhizosphere interactions in intercropping systems. Therefore, we performed a field experiment by growing faba bean, lupine, and maize in mono and mixed cultures in a moderately fertile soil. We measured shoot biomass and the kinetic parameters (maximal velocity (Vmax) and Michaelis-constant (Km)) of three key enzymes in the rhizosphere: Leucine-aminopeptidase (LAP), β-1,4-N-acetylglucosaminidase (NAG), and phosphomonoesterase (PHO). Faba bean benefitted in mixed cultures by greater shoot biomass production with both maize and lupine compared to its expected biomass in monoculture. Next, LAP and NAG kinetic parameters were less responsive to mono and mixed cultures across the crop species. In contrast, both the Vmax and Km values of PHO increased in the faba bean rhizosphere when grown in mixed cultures with maize and lupine. A positive relative interaction index for shoot P and N uptake for faba bean showed its net facilitative interactions in the mixed cultures. Overall, these results suggest that over-productivity in intercropping is crop-specific and the positive intercropping effects could be modulated by P availability. We argue that the enzyme activities involved in nutrient cycling should be incorporated in further research.

    Dan Liu, Guohua Liu, Li Chen, Wangya Han, Dongbo Wang
    Soil Ecology Letters, 2022, 4(4): 454-469.

    • Soil fungal community composition varied significantly between study sites.

    • Plant species richness (PSR) contributed most to the variation in soil fungi community.

    • Both α and β diversity of soil fungi coupled well with that of plant.

    • Plant diversity can predict soil fungal diversity in the temperate steppe of northeastern China.

    Soil fungi and aboveground plant play vital functions in terrestrial ecosystems, while the relationship between aboveground plant diversity and the unseen soil fungal diversity remains unclear. We established 6 sites from the west to the east of the temperate steppe that vary in plant diversity (plant species richness: 7-32) to explore the relationship between soil fungal diversity and aboveground plant diversity. Soil fungal community was characterized by applying 18S rRNA gene sequencing using MiSeq PE300 and aligned with Silva 132 database. As a result, soil fungal community was predominately composed of species within the Ascomycota (84.36%), Basidiomycota (7.22%) and Mucoromycota (6.44%). Plant species richness occupied the largest explanatory power in structuring soil fungal community (19.05%–19.78%). The alpha (α) diversity of the whole soil fungi and Ascomycota showed a hump-backed pattern with increasing plant species richness, and the beta (β) diversity of the whole soil fungi and Ascomycota increased with increasing plant β diversity. Those results indicated that soil fungi and external resources were well balanced at the 20-species level of plant and the sites were more distinct in the composition of their plant communities also harbored more distinct soil fungal communities. Thus, plant diversity could predict both soil fungal α and β diversity in the temperate steppe of northeastern China.

    Irene M. Unger, Robert J. Kremer, Kristen S. Veum, Keith W. Goyne
    Soil Ecology Letters, 2022, 4(3): 276-288.

    • Infestations of Lespedeza cuneata alter soil microbial communities and their actions.

    • Soil alterations persisted up to four years after eradication verses a native prairie.

    • Presence of prairie vegetation may not reflect soil microbial recovery from infestation.

    • Legacy effects of invasives may result in protracted impacts on soil microorganisms.

    • Monitoring soil health indicators in prairies undergoing rehabilitation is important.

    Invasive plant species may alter soil characteristics or interact with the soil microbial community resulting in a competitive advantage. Our objectives were to determine: i) if invasive plant species alter soil properties; and ii) the long-term effects of invasive plant species on soil properties and subsequent implications on ecological restoration efforts. We focused on Lespedeza cuneata, a plant that may be allelopathic. Soil samples were collected from four locations in Central Missouri, USA: an old-field with abundant L. cuneata, two reconstructed sites, and a remnant prairie that has never been plowed. Soil health indictors were used to characterize soil properties at these sites. Nearly every soil property differed significantly between the unplowed prairie reference site and the other three sites. The reconstructed sites, however, generally did not differ from the invaded old-field. These results indicate that the reconstructed prairies are not fully recovered. Although above-ground traits, such as the plant community structure, appear similar to the prairie, the soil microbial community structure still resembles that of an invaded old-field site. These results indicate that more time may be needed before soil microbial populations fully recover after invasive plant removal.

    Minghe Jiang, Luan Zhang, Ming Liu, Han Qiu, Shungui Zhou
    Soil Ecology Letters, 2022, 4(2): 155-163.

    • We evaluated effects of fungi on N2O emission in Chinese milk vetch-containing soils.

    • Fungi to contributed to soil N2O production in CMV-amended soils.

    • Fungi accounted for 56% of N2O emission in CMV-amended soils.

    • Fungi may be important contributors to N2O production in CMV-amended soils.

    Fungi play an important role in soil nitrous oxide (N2O) emission in many agricultural soil systems. However, the effect of fungi on N2O emission in Chinese milk vetch (CMV)-containing soils has not been examined sufficiently. This study investigated the contribution of bacteria and fungi to soil N2O emission in CMV-amended soils. We compared soils from an experimental field in the Fujian Academy of Agricultural Sciences that had been treated with 30 000 kg of CMV per 667 m2 per year with one that was not treated with CMV. We incubated soil using cycloheximide and streptomycin to differentiate fungal and bacterial N2O emissions, respectively. Quantitative PCR (qPCR) was performed to investigate bacterial and fungal abundances in the two agricultural soil ecosystems. The contribution of fungi to soil N2O emission in CMV-amended soils was greater than that in non-CMV-amended paddy soils, with fungi accounting for more than 56% of the emissions in CMV-amended soils. Quantitative PCR showed that the ratio of the internal transcribed spacer to 16S rDNA was significantly higher in CMV-amended soils than in non-CMV-amended paddy soils. Furthermore, soil properties, such as pH (P<0.05) and NH4+ concentration (P<0.05), significantly and negatively affected N2O emission by fungi in soil, whereas the total organic carbon (P<0.05) and NO3- concentration (P<0.05) showed significant positive effects. Fungi may be important contributors to N2O production in CMV-amended soils, which may create challenges for mitigating N2O production.

    Yan Wang, Guowei Chen, Yifei Sun, Kun Zhu, Yan Jin, Baoguo Li, Gang Wang
    Soil Ecology Letters, 2022, 4(1): 18-31.

    •Ÿ Bacterial diversity and community structure differed among agricultural practices.

    •Ÿ Crop rotation enhanced bacterial community succession in rhizosphere.

    •Ÿ Bacterial evenness in root zone was highest from no-tillage plot.

    We are only beginning to understand the influence of agricultural practices, together with soil properties and geographic factors, affect bacterial communities and their influence on the soil processes. Here, we quantify how typical agro-practices, i.e., no-tillage, ridge tillage, continuous corn cropping, and crop rotation with corn and bean, and the corresponding soil physicochemical characteristics affect bacterial diversity and community compositions of the rhizosphere and root zone soils. Results show that species richness in the rhizosphere was significantly higher than that in the root zone soils (p<0.05), typically with more abundant Crenarchaeota and Firmicutes populations that are active members for C and N cycling. Specifically, crop rotation compared to other agro-practices was able to mediate soil pH value and the available P and thereby control the bacterial diversity pattern in the rhizosphere (p<0.05), while tillage practices regulated the relative abundance of bacterial populations in root zone soils by varying the soil available N (p<0.05). Analysis of biomarker patterns suggests that the observed differences in bacterial functional capabilities (e.g., nutrient cycling) are strongly related to the physicochemical properties of surrounding soils. Our results highlight the importance of soil-plant interaction in shaping soil bacterial community structure typically in the rhizosphere and root zone soils and also illustrates the challenges in linking soil ecosystem function to microbial processes.

    Yanxia Xu, Junjie Liu, Xuefeng Liu, Hong Li, Zhao Yang, Hongbao Wang, Xinyu Huang, Lan Lan, Yutong An, Lujun Li, Qin Yao, Guanghua Wang
    Soil Ecology Letters, 2022, 4(2): 131-143.

    • 10 years of CC was a cut-off point in separating soil bacterial community structures.

    • Soil pH and P were well associated with changes of diversity and community structures.

    • N fixation bacteria were increased with successive year, but P, K solubilizing bacteria decreased.

    • Monocropped alfalfa simplified the complexity of the cooccurrence networks.

    Alfalfa is a perennial herbaceous forage legume that is remarkably and negatively affected by monocropping. However, the contribution of the changes in bacterial communities to the soil sickness in alfalfa have not been elucidated. Therefore, we investigated bacterial community structures responses to monocropped alfalfa along the chronosequence. Continuous cropping remarkably reduced bacterial alpha diversity and altered community structures, and soil pH, total P and available P were strongly associated with the changes of bacterial diversity and community structures. Intriguingly, 10-year of monocropped alfalfa might be a demarcation point in separating soil bacterial community structures into two obvious groups that containing soil samples collected in less and more than 10-years. The relative abundances of copiotrophic bacteria of Actinobacteria and Gammaproteobacteria were significantly increased with the extension of continuous cropping years, while the oligotrophic bacteria of Armatimonadetes, Chloroflexi, Firmicutes and Gemmatimonadetes showed the opposite changing patterns. Among those altered phyla, Actinobacteria, Chloroflexi, Alphaproteobacteria and Acidobacteria were the most important bacteria which contributed 50.86% of the community variations. Additionally, the relative abundances of nitrogen fixation bacteria of Bradyrhizobium and Mesorhizobium were obviously increased with successive continuous cropping years, while the abundances of Arthrobacter, Bacillus, Burkholderiaceae and Microbacterium with potential functions of solubilizing phosphorus and potassium were remarkably decreased after long-term continuous cropping. Furthermore, bacterial cooccurrence patterns were significantly influenced by continuous cropping years with long-term monocropped alfalfa simplifying the complexity of the cooccurrence networks. These findings enhanced our understandings and provided references for forecasting how soil bacterial communities responses to monocropped alfalfa.

    Renjun Zhou, Hao Wang, Dongdong Wei, Shenzheng Zeng, Dongwei Hou, Shaoping Weng, Jianguo He, Zhijian Huang
    Soil Ecology Letters, 2022, 4(2): 119-130.

    • Positive microbial interaction dominating in sedimentary bacterial and eukaryotic communities.

    • Homogeneous selection process governed the assemblage of both bacterial and eukaryotic communities.

    • Bacterial and eukaryotic diversities were in the reverse correlations with microbial positive interaction.

    Sedimentary bacterial and eukaryotic communities are major components of the aquatic ecosystem. Revealing the linkages between their community structure and interactions is crucial to understand the diversity and functions of aquatic and soil ecosystems. However, how their diversity and assembly contribute to their interactions on time scale is unclear. This study examined sedimentary bacterial and eukaryotic communities in shrimp culture ponds at different culture stages. The most abundant bacteria were Proteobacteria (38.27%), whereas the most abundant eukaryotes were Chytridiomycota (27.48%). Bacterial and eukaryotic diversities were correlated (P<0.05), implying the strong interactions between bacteria and eukaryotes. Results showed that the bacterial and eukaryotic communities became increasingly similar on a local scale along with the shrimp culture. Only the eukaryotic community significantly increased in similarity along with the shrimp culture (P<0.05), suggesting that the sedimentary eukaryotic community structure is sensitive under shrimp culture. Co-occurrence network modeling indicated that positive microbial interactions were dominant. The homogeneous selection was the major driver of community assembly. Bacterial diversity negatively correlated with operational taxonomic units and positive links in networks (P<0.05), whereas eukaryotic diversities positively correlated with positive links in networks (P<0.05). This study broadens our knowledge about sedimentary microbial diversity, community assembly, and interaction patterns on time scale, providing a reference for the sustainable management in aquaculture production.

    Shuzhen Li, Xiongfeng Du, Kai Feng, Yueni Wu, Qing He, Zhujun Wang, Yangying Liu, Danrui Wang, Xi Peng, Zhaojing Zhang, Arthur Escalas, Yuanyuan Qu, Ye Deng
    Soil Ecology Letters, 2022, 4(3): 224-236.

    • Roughly 15 919 to 56 985 prokaryotic species inhabited in 1 m2 grassland topsoil.

    • Three clustering tools, including DADA2, UPARSE and Deblur showed huge differences.

    • Nearly 500 000 sequences were required to catch 50% species.

    • Insufficient sequencing depth greatly affected observed and estimated richness.

    • Higher order of Hill numbers reached saturation with fewer than 100 000 sequences.

    Due to the tremendous diversity of microbial organisms in topsoil, the estimation of saturated richness in a belowground ecosystem is still challenging. Here, we intensively surveyed the 16S rRNA gene in four 1 m2 sampling quadrats in a typical grassland, with 141 biological or technical replicates generating over 11 million sequences per quadrat. Through these massive data sets and using both non-asymptotic extrapolation and non-parametric asymptotic approaches, results revealed that roughly 15 919±193 27 193±1076 and 56 985±2347 prokaryotic species inhabited in 1 m2 topsoil, classifying by DADA2, UPARSE (97% cutoff) and Deblur, respectively, and suggested a huge difference among these clustering tools. Nearly 500 000 sequences were required to catch 50% species in 1 m2, while any estimator based on 500 000 sequences would still lose about a third of total richness. Insufficient sequencing depth will greatly underestimate both observed and estimated richness. At least ~911 000, ~3 461 000, and ~1 878 000 sequences were needed for DADA2, UPARSE, and Deblur, respectively, to catch 80% species in 1 m2 topsoil, and the numbers of sequences would be nearly twice to three times on this basis to cover 90% richness. In contrast, α-diversity indexes characterized by higher order of Hill numbers, including Shannon entropy and inverse Simpson index, reached saturation with fewer than 100 000 sequences, suggesting sequencing depth could be varied greatly when focusing on exploring different α-diversity characteristics of a microbial community. Our findings were fundamental for microbial studies that provided benchmarks for the extending surveys in large scales of terrestrial ecosystems.

    Yifei Sun, Meiling Sun, Guowei Chen, Xin Chen, Baoguo Li, Gang Wang
    Soil Ecology Letters, 2021, 3(4): 313-327.

    • Relative abundances of microbial communities were most related to aggregate proportions in clay-layer soils.

    • Aggregate content with<0.053 mm in clay-layer soil significantly influence the diversity of soil microbial community.

    • Complexity of microbial interactions raised along increasing precipitation across sampling sites.

    • Competition for substrates induced niche differentiation in deeper soils.

    Soil microorganisms play a key role in the function of soil ecosystem, yet our knowledge about how microbial communities respond to the typically sandy soil environmental properties along the soil profile is still insufficient. We investigated the soil microbial community patterns from top (0 – 20 cm) to clay-layer (>80 cm) of the typical sandy soils in three regions in China with different levels of precipitation, including Lishu County in Jilin Province (LS), Langfang City in Hebei Province (LF) and Zhengzhou City in Henan Province (ZZ). Our findings showed that small-size aggregates (<0.5 mm) rather than large ones (>= 0.5 mm) dominated the soil profile. The relative abundances of Actinobacteria, Crenarchaeota and Firmicutes were highly related to aggregate proportions of the deep clay-layer soil. The network analysis revealed the distinct community patterns among modules, evidencing niche differentiation along the soil profile. The keystone species OTU_11292 was observed having migrated clearly into the other module of the clay-layer soil. Different roles of the OTU_30 (belonging to Gemmatimonadetes) in soil processes might partly explain the different microbial distribution between top- and clay-layer soils. These findings provided new insights into the candidate mechanisms of microbial diversity maintenance and community patterning of sandy soils, which were necessary for better understanding of ecological rules guiding long-term agricultural practice.

    Sabrina M. Pittroff, Stefan Olsson, Ashlea Doolette, Ralf Greiner, Alan E. Richardson, Mette Haubjerg Nicolaisen
    Soil Ecology Letters, 2021, 3(4): 367-382.

    • A novel microcosm for identifying phytate-degrading soil microbes is introduced

    • Phytate microcosms recruited different microbial profiles when compared to controls

    • Microbial populations recruited by phytate showed phosphatase activity in vitro

    • Streptomyces were indicated as inherently competitive in solum utilizers of phytate

    Fertilizer phosphorus (P) is a finite resource, necessitating the development of innovative solutions for P fertilizer efficiency in agricultural systems. Myo-inositol hexakisphosphate (phytate) constitutes the majority of identified organic P in many soil types and is poorly available to plants. Incorporating phytase-producing biofertilizers into soil presents a viable and environmentally acceptable way of utilizing P from phytate, while reducing the need for mineral P application. A deeper understanding of the microbial ecology in relation to degradation of phytate under natural soil conditions is however needed to obtain successful biofertilizer candidates able to compete in complex soil environments. Here we present the development of a microcosm for studying microbial communities able to colonize and utilize Ca-phytate hotspots in solum. Our results provide evidence that the recruited microbial population mineralizes Ca-phytate. Furthermore, quantification of bacterial genes associated with organic P cycling in alkaline soils indicated that the phosphatases PhoX and PhoD may play a larger role in phytate mineralization in soil than previously recognized. Amplicon sequencing and BioLog® catabolism studies show that hotspots containing Ca-phytate, recruited a different set of microorganisms when compared to those containing an addition of C source alone, with the genus Streptomyces specifically enriched. We propose that Streptomyces represents an hitherto unexplored resource as P biofertilizer with competitive advantage for utilizing CaPhy in an inherently competitive soil environment. We further conclude that the use of our newly designed microcosm presents an innovative approach for isolating soil microorganisms with the potential to degrade precipitated phytate in solum.

    Tao Wen, Mengli Zhao, Jun Yuan, George A. Kowalchuk, Qirong Shen
    Soil Ecology Letters, 2021, 3(1): 42-51.

    •Ÿ Long-chain fatty acids and amino acids application could form foliar disease resistant-soil microbial community

    •Ÿ Population of Pseudomonas was enriched by long-chain fatty acids and amino acids application

    •Ÿ The enriched Pseudomonas could help plant resistant foliar pathogens.

    Plants are capable of releasing specific root exudates to recruit beneficial rhizosphere microbes upon foliar pathogen invasion attack, including long-chain fatty acids, amino acids, short-chain organic acids and sugars. Although long-chain fatty acids and amino acids application have been linked to soil legacy effects that improve future plant performance in the presence of the pathogen, the precise mechanisms involved are to a large extent still unknown. Here, we conditioned soils with long-chain fatty acids and amino acids application (L+ A) or short-chain organic acids and sugars (S+ S) to examine the direct role of such exudates on soil microbiome structure and function. The L+ A treatment recruited higher abundances of Proteobacteria which were further identified as members of the genera Sphingomonas, Pseudomonas, Roseiflexus, and Flavitalea. We then isolated the enriched bacterial strains from these groups, identifying ten Pseudomonas strains that were able to help host plant to resist foliar pathogen infection. Further investigation showed that the L+ A treatment resulted in growth promotion of these Pseudomonas strains. Collectively, our data suggest that long-chain fatty acids and amino acids stimulated by foliar pathogen infection can recruit specific Pseudomonas populations that can help protect the host plant or future plant generations.

    Haifeng Qian, Qi Zhang, Tao Lu, W.J.G.M. Peijnenburg, Josep Penuelas, Yong-Guan Zhu
    Soil Ecology Letters, 2021, 3(1): 1-5.
    Jianing Wang, Xinlan Mei, Zhong Wei, Waseem Raza, Qirong Shen
    Soil Ecology Letters, 2021, 3(1): 32-41.

    Microorganisms experience intra- and inter-species interactions in the soil, and how these interactions affect the production of microbial volatile organic compounds (VOCs) is still not well-known. Here we evaluated the production and activity of microbial VOCs as driven by bacterial intra-species community interactions. We set up bacterial communities of increasing biodiversity out of 1–4 strains each of the Gram-positive Bacillus and Gram-negative Pseudomonas genera. We evaluated the ability of each community to provide two VOC-mediated services, pathogen suppression and plant-growth promotion and then correlated these services to the production of VOCs by each community. The results showed that an increase in community richness from 1 to 4 strains of both genera increased VOC-mediated pathogen suppression and plant-growth promotion on agar medium and in the soil, which was positively correlated with the production of pathogen suppressing and plant growth-promoting VOCs. Pseudomonas strains maintained while Bacillus strains reduced community productivity with an increase in community richness and produced eight novel VOCs compared with the monocultures. These results revealed that intra-species interactions may vary between Gram-negative and Gram-positive species but improved VOC-mediated functioning with respect to pathogen suppression and plant-growth promotion by affecting the amount and diversity of produced VOCs potentially affecting plant disease outcomes.

    Zhijing Xue, Zhengchao Zhou, Shaoshan An
    Soil Ecology Letters, 2021, 3(1): 6-21.

    • The soil aggregate stability increased with increasing duration of vegetation restoration.

    • Natural restoration has a positve effect on soil microbial diversity was generally higher in large particle size aggregates, which leads to low environmental stress and strong stability.

    • Microorganism continually changed their regulation of pathways as their environment changed.

    • Environment adaptability influences soil physiological indicators to varying degrees.

    • After years of natural restoration, the soil microbial community generally transformed from nutrient-rich to heterotroph-dominan.

    Soil aggregate fractions can regulate microbial community composition and structure after vegetation restoration. However, there has been less focus on the effects of soil aggregate fractions on the distributions of microbial communities. Here, we used phospholipid fatty acid (PLFA) analysis to explore the effects of different years of vegetation restoration (a 35-year-old Thymus mongolicus community (Re-35yrs) and a 2-year-old nongrazing grassland (Ug-2yrs)) on microbial communities within different soil aggregate sizes (<0.25 mm, 0.25–1 mm, 1–2 mm, 2–3 mm, 3–5 mm and>5 mm). The results indicated that the amount of total PLFA in Re-35yrs was 10 times greater than that in Ug-2yrs. The soil aggregate stability increased with increasing duration of vegetation restoration. In Re-35yrs, the total PLFA shown an increase as the soil aggregate size increased, and the highest values were observed in 3~5 mm. Ug-2yrs differed from Re-35yrs, the soil microbial diversity was higher in medium particle sizes (1–2 mm and 2–3 mm) and lower in microaggregates (<0.25 mm and 0.25–1 mm) and macroaggregates (3~5 mm and>5 mm). Soil microbial diversity was highest in large particle size aggregates, which resulted in low environmental stress and strong stability. The same tendency was observed in the high values of cyc/prec, S/M and soil organic matter, which indicated a lower turnover speed (F/B) of fungal energy utilization and a higher fixation rate. After years of natural restoration, the soil microbial community generally transformed from nutrient-rich to heterotroph-dominant, especially in microaggregates (reflected in the G+/G ratio).