Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction

Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances

Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.

Effects of pyrolysis temperature on soil-plant-microbe responses to Solidago canadensis L.-derived biochar in coastal saline-alkali soil

Because salinity of coastal soils is drastically increasing, the application of biochars to saline-alkali soil amendments has attracted considerable attention. Various Solidago-canadensis-L.-derived biochars prepared through pyrolysis from 400 to 600 °C were applied to coastal saline-alkali soil samples to optimise the biochar pyrolysis temperature and investigate its actual ecological responses. All biochars reduced the soil bulk density and exchangeable sodium stress and increased soil water-holding capacity, cation exchange capacity, and organic matter content. Principal-component-analysis results showed that pyrolysis temperature played an important role in the potential application of biochars to improve the coastal saline-alkali soil, mainly contributed to ameliorating exchangeable sodium stress and decreasing biochar-soluble toxic compounds. Furthermore, soil bulk density and organic matter, as well as carboxylic acids, phenolic acids and amines of biochar were major driving factors for bacterial community composition. Compared to low-temperature biochar (pyrolyzed below 550 °C), which showed higher toxicity for Brassica chinensis L. growth due to the higher content of carboxylic acids, phenols and amines, high-temperature biochar (pyrolyzed at or above 550 °C) possessed less amounts of these toxic functional groups, more beneficial soil bacteria and healthier for plant growth. Therefore, high-temperature biochar could be applied as an effective soil amendment to ameliorate the coastal saline-alkali soil with acceptable environmental risk.

Effects of Zinc Pollution and Compost Amendment on the Root Microbiome of a Metal Tolerant Poplar Clone

Until recently, many phytoremediation studies were focused solely on a plants ability to reclaim heavy metal (HM) polluted soil through a range of different processes, such as phytoextraction and phytostabilization. However, the interaction between plants and their own rhizosphere microbiome represents a new research frontier for phytoremediation. Our hypothesis is that rhizomicrobiome might play a key role in plant wellness and in the response to external stimuli; therefore, this study aimed to shed light the rhizomicrobiome dynamics after an organic amendment (e.g., compost) and/or HM pollution (e.g., Zn), and its relation with plant reclamation ability. To reach this goal we set up a greenhouse experiment cultivating in pot an elite black poplar clone (N12) selected in the past for its excellent ability to reclaim heavy metals. N12 saplings were grown on a soil amended with compost and/or spiked with high Zn doses. At the end of the experiment, we observed that the compost amendment strongly increased the foliar size but did not affect significantly the Zn accumulation in plant. Furthermore, the rhizomicrobiome communities (bacteria and fungi), investigated through NGS, highlighted how α diversity increased in all treatments compared to the untreated N12 saplings. Soil compost amendment, as well as Zn pollution, strongly modified the bacterial rhizomicrobiome structure. Conversely, the variation of the fungal rhizomicrobiome was only marginally affected by soil Zn addition, and only partially impaired by compost. Nevertheless, substantial alterations of the fungal community were due to both compost and Zn. Together, our experimental results revealed that organic amendment increased the bacterial resistance to external stimuli whilst, in the case of fungi, the amendment made the fungi microbiome more susceptible. Finally, the greater microbiome biodiversity does not imply, in this case, a better plant wellness or phytoremediation ability, although the microbiome plays a role in the external stimuli response supporting plant life.

Dam Construction as an Important Anthropogenic Activity Disturbing Soil Organic Carbon in Affected Watersheds

To explore whether and how anthropogenic activities related to surface water regulation (i.e., dam construction) disturb soil ecosystems in the surrounding uplands, a long-term monitoring program was conducted from 1998 to 2017 in the Three Gorges Reservoir Region, China. The Three Gorges Dam (TGD) is the largest hydraulic engineering project in the world. We present a direct, ecosystem-scale demonstration of changes in the soil organic carbon (SOC) content in the TGD watershed before and after the surface water was reshaped. The average SOC content decreased from 12.9 to 9.5 g/kg between 2004 and 2012 and then recovered to 13.8 g/kg in 2017. Dynamics of SOC were partly attributed to shifts in the composition of soil microbial communities responsible for carbon biogeochemistry. The shifts in microbial taxa were associated with the changed microclimate affected by the TGD as well as global and regional climate variability. The microclimate, soil microorganisms, and plant organic carbon input explained 40.2% of the variation in the SOC content. This study revealed that dam construction was an important and indirect driver for the SOC turnover, and the subsequent effects on the upland soil ecosystem must be considered when large-scale disturbance activities (such as dam construction) are conducted in the future.

Differences in substrate use linked to divergent carbon flow during litter decomposition

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

Effects of biochar-based controlled release nitrogen fertilizer on nitrogen-use efficiency of oilseed rape (Brassica napus L.)

Biochar-based controlled release nitrogen fertilizers (BCRNFs) have received increasing attention due to their ability to improve nitrogen-use efficiency (NUE) and increase crop yields. We previously developed a novel BCRNF, but its effects on soil microbes, NUE, and crop yields have not been reported. Therefore, we designed a pot experiment with five randomised treatments: CK (without urea and biochar), B (addition biochar without urea), B + U (biochar mixed urea), Urea (addition urea without biochar), and BCRNF (addition BCRNF), to investigate the effects of BCRNF on nitrifiers and denitrifiers, and how these impact nitrogen supply and NUE. Results of high-throughput sequencing revealed bacterial community groups with higher nutrient metabolic cycling ability under BCRNF treatment during harvest stage. Compared to Urea treatment, BCRNF treatment stimulated nitrification by increasing the copy number of the bacterial amoA gene and reducing nitrous oxide emission by limiting the abundance of nirS and nirK. Eventually, BCRNF successfully enhanced the yield (~ 16.6%) and NUE (~ 58.79%) of rape by slowly releasing N and modulating the abundance of functional microbes through increased soil nitrification and reduced denitrification, as compared with Urea treatment. BCRNF significantly improved soil NO₃⁻, leading to an increase in N uptake by rape and NUE, thereby promoting rape growth and increasing grain yield.

Habitat-specific environmental factors regulate spatial variability of soil bacterial communities in biocrusts across northern China's drylands

Biocrusts are common biotic components in dryland ecosystems worldwide, they contain diverse soil organisms and effectively enhance soil stability and perform a series of key ecological functions. However, the geographical pattern of microbial communities in biocrusts is rarely assessed, despite it is closely related to the spatial variation of ecosystem functions in drylands. We assessed soil bacterial communities in biocrusts across four ecosystems (Gobi, desert, desert steppe and grassland) in a precipitation gradient (16-566 mm yr^-1) in northern China. Bacterial OTU number and phylogenetic diversity did not linearly increase with decreasing aridity, they were significantly lower in Gobi and similar among desert, desert steppe and grassland. Soil bacterial community composition in Gobi and desert were different than those in desert steppe and grassland, and they were similar between Gobi and desert, this suggests the key role of habitat in structuring soil bacterial communities. The geographic pattern of soil bacterial communities was strongly influenced by both geographic distance and environmental factors. The first explanatory factor for the geographic variation of bacterial community dissimilarity differed among four ecosystems, being aridity in Gobi and desert, precipitation in desert steppe, and soil inorganic nitrogen in grassland. The geographic pattern of the bacterial functional group profile showed a similar pattern with community composition across four ecosystems, and the groups of containing mobile elements and gram negative bacteria were more abundant in drier habitats of Gobi and desert. Our results reveal the non-linear changes in diversity, composition and functional group of soil bacterial communities in biocrusts across the precipitation gradient from hyper-arid to semi-humid regions, and suggest that the geographic distance and habitat-specific environmental factors determine the distribution of soil bacterial communities in different ecosystems.

Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani

Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.

Exploring the effect of plant substrates on bacterial community structure in termite fungus-combs

Fungus-cultivating termites are successful herbivores largely rely on the external symbiotic fungus-combs to decompose plant polysaccharides. The comb harbors both fungi and bacteria. However, the complementary roles and functions of the bacteria are out of the box. To this purpose, we look into different decomposition stages of fungus-combs using high-throughput sequencing of the 16S rRNA gene to examine bacterial community structure. We also explored the bacterial response to physicochemical indexes (such as moisture, ash content and organic matter) and plant substrates (leaves or branches or mix food). Some specific families such as Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae may be involved in lignocellulose degradation, whereas Burkholderiaceae may be associated with aromatic compounds degradation. We observed that as the comb mature there is a shift of community composition which may be an adjustment of specific bacteria to deal with different lignocellulosic material. Our results indicated that threshold amount of physicochemical indexes are beneficial for bacterial diversity but too high moisture, low organic matter and high ash content may reduce their diversity. Furthermore, the average highest bacterial diversity was recorded from the comb built by branches followed by mix food and leaves. Besides, this study could help in the use of bacteria from the comb of fungus-cultivating termites in forestry and agricultural residues making them easier to digest as fodder.

Mikania micrantha invasion enhances the carbon (C) transfer from plant to soil and mediates the soil C utilization through altering microbial community

Exotic plant invasion alters the structure and coverage of terrestrial vegetation and affects the carbon (C) stocks in ecosystems. Previous studies have shown the increases in the C stocks with increasing invasive plants, but these results remain contentious. Soil microbial communities are usually altered by plant invasion, which potentially influences the C cycling underground. We hypothesized that the plant invasion-caused dynamic changes in soil microbes would lead to the corresponding change in soil C accumulation. Using greenhouse experiments we simulated different invader intensities through varying the relative abundance of invasive species Mikania micrantha and its co-occurring native species Paederia scandens. By analyzing ¹³C-phospholipid fatty acid we found the invasive M. micrantha assimilated more ¹³C and transferred faster the fixed ¹³C through different tissues to soils, as compared to native P. scandens. Soil microbial components, i.e., i15:0, 16:0, 10Me16:0, 18:1w9c and 18:2w6,9 were mainly using the photo-assimilated ¹³C. In addition, we found a hump-shaped relationship between soil net ¹³C accumulate rate and rhizosphere microbial biomass, indicating that the soil C accumulation may be either enhanced or reduced in invaded ecosystems, depending on microbe abundance.

Impact of topsoil removal on soil CO2 emission and temperature sensitivity in Chinese Loess Plateau

Soil redistribution by terrace construction, as one of the most evident anthropogenic imprints on hill-slopes, may influence soil organic carbon (SOC) dynamics through re-shaping topography and altering water and oxygen availability. However, the fundamental role and mechanisms by which terrace construction affects in situ soil CO₂ emissions and its temperature sensitivity (Q₁₀) remain poorly understood. In this study, topsoil removal-addition approach was used to simulate topsoil redistribution during terrace construction. Compared with the nearby undisturbed soil, the average annual soil CO₂ emission over two years was reduced by 24% in the topsoil removed field but enhanced by 33% in the topsoil added field. The decreased soil CO₂ emission at the topsoil removed field was largely associated with the depletion of SOC stocks and microbial biomass carbon, while the increments of SOC available for decomposition at the topsoil added field contributed to its increased soil CO₂ emissions. However, the average Q₁₀ value in the topsoil removed field was 23% greater at seasonal scale and 28% greater at diurnal scale than that in the undisturbed soil. The increased Q₁₀ in the topsoil removed field is mainly due to higher aromaticity of water-extractable organic carbon (WEOC) and the domination of Actinobacteria in keystone taxa. Overall, our results show that changes in both aromaticity of WEOC and soil microbial community composition induced by soil redistribution during terrace construction may alter the response of soil CO₂ emission to elevated temperature. Our study indicates that the impact of man-made soil redistribution should not be neglected when studying regional carbon cycling.

Disturbance, carbon physicochemical structure, and soil microenvironment codetermine soil organic carbon stability in oilfields

The stability of soil organic carbon (SOC) is crucial for soil quality, fertility, and natural attenuation processes of pollutants. The physicochemical structures of SOC were believed to control its stability, yet has become controversial. Here we hypothesized that disturbance intensity and variations in the soil environment can also influence the SOC stability, and conducted a case study with oil contaminated soils to quantify the contributions to SOC stability of various factors including contamination level, carbon physicochemical structure, and soil properties. Oil contamination led to increased SOC stability, as suggested by appreciably decreased soil CO₂ fluxes, the enrichment of the δ¹³C in the oil contaminated soils, as well as analysis of soil aggregates and humic substances. Redundancy analysis indicated that overall SOC stability were highly correlated to microaggregate (M2), HA/FA, Fe, soil porosity, EC, pH, and total petroleum hydrocarbon (TPH) in oilfields. Variance partitioning analysis showed that carbon physicochemical structure (S), soil properties (P), and oil contamination (O) could explain the variance of overall SOC stability by up to 90%, while 18% of the variation was explained by S × P and 43% by S × P × O. These results show that multiple factors of the disturbance, carbon physicochemical structure, and soil properties should be essential for future studies of SOC stability.

Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance

BACKGROUND

Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members.

RESULTS

Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor's nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community.

CONCLUSIONS

Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.

Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide

Advances in technologies for molecular observation are leading to novel types of data, including gene, transcript, protein, and metabolite levels, which are fundamentally different from the types traditionally compared with microbial ecosystem models, such as biomass (e.g., chlorophyll a) and nutrient concentrations. A grand challenge is to use these data to improve predictive models and use models to explain observed patterns. This article presents a framework that aligns observations and models along the dimension of abstraction or biological organization-from raw sequences to ecosystem patterns for observations, and from sequence simulators to ecological theory for models. It then reviews 16 studies that compared model results with molecular observations. Molecular data can and are being combined with microbial ecosystem models, but to keep up with and take advantage of the full scope of observations, models need to become more mechanistically detailed and complex, which is a technical and cultural challenge for the ecological modeling community.

Evidence for positive response of soil bacterial community structure and functions to biosynthesized silver nanoparticles: An approach to conquer nanotoxicity?

The environmental impacts of biosynthesized nanoparticles on the soil bacterial community assemblage and functions are not sufficiently understood. Given the broad application of silver nanoparticles (AgNPs), the present study aims to reveal the effects of biosynthesized AgNPs (~12 nm) on the soil bacterial community structure and functions. Specifically, we used a quantitative real-time PCR (qPCR) approach to quantify the relative abundance of bacterial taxon/group and representative functional genes (AOA, AOB, NirK, NirS, NosZ, and PhoD). Results showed high relative abundance of Actinobacteria (1.53 × 10⁷, p = 0.000) followed by Alphaproteobacteria (1.18 × 10⁶, p = 0.000) and Betaproteobacteria (2.01 × 10⁶, p = 0.000) in the soil exposed to biosynthesized AgNPs (100 mg/kg soil) after 30 days of treatment. Bacteroidetes group was observed to be negatively affected by AgNPs treatment. In the case of functional genes abundance, more pronounced impact was observed after 30 days of application. The biosynthesized AgNPs treatment accounted for significant increase in the relative abundance of all targeted functional genes except NirS. We conclude that the biosynthesized AgNPs did not cause toxic effects on nitrifiers, denitrifiers and organic phosphorus metabolizing bacterial community. While AgNO₃ caused higher toxicity in the soil bacterial community structure and function. Based on our findings, we propose two key research questions for further studies; (i) is there any adaptation strategy or silver resistance embraced by the soil microbial community? and (ii) are biosynthesized nanoparticles environmentally safe and do not pose any risk to the soil microbial community? There is a necessity to address these questions to predict the environmental safety of biosynthesized AgNPs and to apply appropriate soil management policies to avoid nanotoxicity. Since this study provides preliminary evidence for the positive response of the soil bacterial community structure and functions to biosynthesized AgNPs, additional investigations under different soil conditions with varying soil physico-chemical properties are required to authenticate their environmental impact.

Suppressed N fixation and diazotrophs after four decades of fertilization

BACKGROUND

N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization.

RESULTS

It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp.

CONCLUSIONS

Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.

Intra-horizon differentiation of the bacterial community and its co-occurrence network in a typical Plinthic horizon

Subsurface soil bacterial community composition and the controlling factors remain largely unknown, especially the micro-zone differentiation of community composition within a horizon. We studied a plinthic horizon to determine how different micro-zones in a horizon affect the bacterial community. The plinthic horizon is a net-like horizon characterized by the segregation of iron forms as shown by contrasting red matrix and white veins, which share common macro-environmental conditions such as climate and land use but differ only in physical and chemical compositions. The studied horizon is typical of the red soils of southeastern China and is an important layer in the red soil Critical Zone. The plinthite is considered to have been formed in the Quaternary and thus is a record of the paleo-environment. We evaluated the difference in the bacterial community composition between the red matrix and white veins and explored the possible assembly mechanisms of their co-occurrence patterns. Compared to the eutrophic environments of a red matrix, higher relative abundances of Acidobacteria and Nitrospirae were observed in the white veins. Similarly, more niches led to a higher density of bacterial co-occurrence patterns in the red matrix. The differences in the bacterial community composition and association networks are due to environmental selection, including the legacy of the paleoclimate that is represented by major element contents and contemporary hydrological properties that are mainly controlled by the soil texture. Our study shows that micro-zones even within a same plinthic horizon can provide different habitats and thus select for specific bacterial communities. Furthermore, this study could improve our understanding of the differentiation of bacterial communities among microenvironments caused by both historical and contemporary processes and help to predict how these communities may respond to future environmental changes.

The Impact of Near Natural Forest Management on the Carbon Stock and Sequestration Potential of Pinus massoniana (Lamb.) and Cunninghamia lanceolata (Lamb.) Hook. Plantations

Quantifying the impact of forest management on carbon (C) stock is important for evaluating and enhancing the ability of plantations to mitigate climate change. Near natural forest management (NNFM) through species enrichment planting in single species plantations, structural adjustment, and understory protection is widely used in plantation management. However, its long-term effect on forest ecosystem C stock remains unclear. We therefore selected two typical coniferous plantations in southwest China, Pinus massoniana (Lamb.) and Cunninghamia lanceolate (Lamb.) Hook., to explore the effects of long-term NNFM on ecosystem C storage. The C content and stock of different components in the pure plantations of P. massoniana (PCK) and C. lanceolata (CCK), and their corresponding near natural managed forests (PCN and CCN, respectively), were investigated during eight years of NNFM beginning in 2008. In 2016, there was no change in the vegetation C content, while soil C content in the 0–20 cm and 20–40 cm layers significantly increased, compared to the pure forests. In the P. massoniana and C. lanceolata plantations, NNFM increased the ecosystem C stock by 31.8% and 24.3%, respectively. Overall, the total C stock of soil and arborous layer accounted for 98.2%–99.4% of the whole ecosystem C stock. The increase in the biomass of the retained and underplanted trees led to a greater increase in the arborous C stock in the near natural forests than in the controls. The NNFM exhibited an increasingly positive correlation with the ecosystem C stock over time. Long-term NNFM enhances ecosystem C sequestration by increasing tree growth rate at individual and stand scales, as well as by likely changing the litter decomposition rate resulting from shifts in species composition and stand density. These results indicated that NNFM plays a positive role in achieving multi-objective silviculture and climate change mitigation.

Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions

Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.

Ant colonies promote the diversity of soil microbial communities

Little is known about the role of ant colonies in regulating the distribution and diversity of soil microbial communities across large spatial scales. Here, we conducted a survey across >1000 km in eastern Australia and found that, compared with surrounding bare soils, ant colonies promoted the richness (number of phylotypes) and relative abundance of rare taxa of fungi and bacteria. Ant nests were also an important reservoir for plant pathogens. Our study also provides a portfolio of microbial phylotypes only found in ant nests, and which are associated with high nutrient availability. Together, our work highlights the fact that ant nests are an important refugia for microbial diversity.

The structure and function of the global citrus rhizosphere microbiome

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions

Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa,” i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.

Short-term biochar manipulation of microbial nitrogen transformation in wheat rhizosphere of a metal contaminated Inceptisol from North China plain

While metal immobilization had been increasingly reported with biochar soil amendment (BSA), changes in microbial activity and nitrogen (N) transformation in metal contaminated croplands following biochar addition had been insufficiently addressed. In a field experiment, a Pb/Cd contaminated Inceptisol from North China was amended to topsoil with wheat straw biochar at 0 (CK), 20 (C1) and 40 t ha^-1 (C2). The changes within two years following BSA were tested in microbial biomass and respiration, and in abundance of N transforming microbial communities and their activities. Corresponding to the results of decreased soil extractable Cd and Pb, significant reductions in qCO₂ were found in rhizosphere and bulk soil only under C2 in the first year. The potential nitrification activity was significantly increased by 20-71%, along with an increase in ammonium (by 7-21%) and nitrate (by 21%-70%) concentration, with BSA compared to CK. Meanwhile, N₂O production activity was slightly increased (by up to 20%) but N₂O reduction activity greatly enhanced (by up to 84%), with a higher ratio of nosZ/(nirS + nirK), under C2 in rhizosphere in both wheat seasons. Whereas, such changes were not remarkable in bulk soil. Moreover, microbial communities were less respondent to biochar in the second year following the addition. Therefore, microbial growth and functioning for N transforming and cycling in metal contaminated soils could be largely improved with BSA at 40 t ha^-1. Of course, studies are still deserved to mimic the long term changes with biochar in N cycling of the metal contaminated dry croplands.

Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents

Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands.

Fate of di (2‑ethylhexyl) phthalate in different soils and associated bacterial community changes

Di (2‑ethylhexyl) phthalate (DEHP) is a ubiquitous organic pollutant, which has caused considerable pollution in arable soils. In this study, the relationship between DEHP degradation potential and soil properties in 12 agricultural soils (S1-S12) was examined in a microcosm based experiment. Six of these soils were then selected to monitor patterns in bacterial community responses. It was found that DEHP degradation was positively correlated with bacterial counts in the original soils, suggesting a key role for bacteria in degradation. However, DEHP metabolism did not always lead to complete degradation. Its monoester metabolite, mono (2‑ethylhexyl) phthalate (MEHP), was present at appreciable levels in the two acidic soils (S1 and S2) during the incubation period of 35 days. Based on high-throughput sequencing data, we observed a greater impact of DEHP contamination on bacterial community structure in acidic soils than in the other soils. Nocardioides, Ramlibacter and unclassified Sphingomonadaceae were enriched in the two near-neutral soils where degradation was highest (S4 and S7), suggesting that these organisms might be efficient degraders. The relative abundance of Tumibacillus was greatly reduced in 50% of the six soils examined, demonstrating a high sensitivity to DEHP contamination. Furthermore, putative organic-matter decomposing bacteria (including Tumebacillus and other bacteria taxa such as members from Micromonosporaceae) were greatly reduced in the two acidic soils (S1 and S2), possibly due to the accumulation of MEHP. These results suggest a crucial role of soil acidity in determining the fate and impact of DEHP in soil ecosystems, which deserves further investigation. This work contributes to a better understanding of the environmental behavior of DEHP in soil and should facilitate the development of appropriate remediation technologies.

Contrasting responses of bacterial and fungal communities to aggregate-size fractions and long-term fertilizations in soils of northeastern China

Soils, with non-uniform distribution of nutrients across different aggregate-size fractions, provide spatially heterogeneous microhabitats for microorganisms. However, very limited information is available on microbial distributions and their response to fertilizations across aggregate-size fractions in agricultural soils. Here, we examined the structures of bacterial and fungal communities across different aggregate-size fractions (2000-250 μm, 250-53 μm and <53 μm) in response to 35-years organic and/or chemical fertilization regimes in the soil of northeastern China by phospholipid fatty acid (PLFA) and high throughput sequencing (HTS) technology. Our results show that larger fractions (>53 μm), especially 250-53 μm aggregates, which contain more soil C and N, are associated with greater microbial biomass and higher fungi/bacteria ratio. We firstly reported the fungal community composition in different aggregate-size fractions by HTS technology and found more Ascomycota but less Zygomycota in larger fractions with higher C content across all fertilization regimes. Fertilization and aggregate-size fractions significantly affect the compositions of bacterial and fungal communities although their effects are different. The bacterial community is mainly driven by fertilization, especially chemical fertilizers, and is closely related to the shifts of soil P (phosphorus). The fungal community is preferentially impacted by different aggregate-size fractions and is more associated with the changes of soil C and N. The distinct responses of microbial communities suggest different mechanisms controlling the assembly of soil bacterial and fungal communities at aggregate scale. The investigations of both bacterial and fungal communities could provide a better understanding on nutrient cycling across aggregate-size fractions.

Influence of Altered Microbes on Soil Organic Carbon Availability in Karst Agricultural Soils Contaminated by Pb-Zn Tailings

Soil organic carbon (SOC) availability is determined via a complex bio-mediated process, and Pb-Zn tailings are toxic to the soil microbes that are involved in this process. Here, Pb-Zn-tailings- contaminated karst soils with different levels (paddy field > corn field > citrus field > control group) were collected to explore the intrinsic relationship between Pb-Zn tailings and microbes due to the limited microbial abundance in these soils. The SOC concentration in the paddy fields is the highest. However, based on the soil microbial diversity and sole-carbon-source utilization profiles, the rate of SOC availability, McIntosh index, Shannon-Wiener diversity index, Simpson's diversity index and species richness are the lowest in the rice paddy soils. According to the results of Illumina sequencing of the 16S rRNA gene, Acidobacteria and Proteobacteria are the dominant phyla in all samples, accounting for more than 70% of the reads, while the majority of the remaining reads belong to the phyla Verrucomicrobia, Chloroflexi, Actinobacteria, Bacteroidetes, and Nitrospirae. We also observed that their class, order, family, genus and operational taxonomic units (OTUs) were dependent on SOC availability. Pearson correlation analysis reveals that L-asparagine utilization profiles show significant positive correlation with OTUs 24, 75, and 109 (r = 0.383, 0.350, and 0.292, respectively), and malic acid utilization profiles show significant positive correlation with OTUs 4, 5, 19, 27 (Bradyrhizobium), 32 (Burkholderia), 75 and 109 (r = 0.286, 0.361, 0.387, 0.384, 0.363, 0.285, and 0.301, respectively), as also evidenced by the redundancy analysis (RDA) biplot and heat map. These results indicate that the most abundant groups of bacteria, especially the uncultured facultative Deltaproteobacteria GR-WP33-30 (OTU 24), after long-term acclimation in heavy metal-contaminated soil, are associated with the variance of labile carbon source such as L-asparagine and may have considerable control over the stability of the vast SOC pool in karst surface soils with different agricultural land-use practices. These findings can expand our understanding of global soil-carbon sequestration and storage via changes in microbial community structure of the most abundant species.

Climate-smart crops with enhanced photosynthesis

The potential of enhanced photosynthetic efficiency to help achieve the sustainable yield increases required to meet future demands for food and energy has spurred intense research towards understanding, modeling, and engineering photosynthesis. These current efforts, largely focused on the C3 model Arabidopsis thaliana or crop plants (e.g. rice, sorghum, maize, and wheat), could be intensified and broadened using model systems closely related to our food, feed, and energy crops and that allow rapid design-build-test-learn cycles. In this outlooking Opinion, we advocate for a concerted effort to expand our understanding and improve our ability to redesign carbon uptake, allocation, and utilization. We propose two specific research directions that combine enhanced photosynthesis with climate-smart metabolic attributes: (i) engineering pathways for flexible (facultative) C3-C4 metabolism where plants will operate either C3 or C4 photosynthesis based on environmental conditions such as temperature, light, and atmospheric CO2 levels; and (ii) increasing rhizospheric sink strength for carbon utilization, including strategies that allow for augmented transport of carbon to the soil for improved soil properties and carbon storage without jeopardizing aboveground crop biomass. We argue that such ambitious undertakings be first approached and demonstrated by exploring the full genomic potential of two model grasses, the C3Brachypodium distachyon and the C4Setaria viridis. The development of climate-smart crops could provide novel and bold solutions to increase crop productivity while reducing atmospheric carbon and nitrogen emissions.

Microbial functional gene patterns related to soil greenhouse gas emissions in oil contaminated areas

Linking microbial community structure to physiology and ecological processes is a critical focus of microbial ecology. To understand the microbial functional gene patterns related to soil greenhouse gas [carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O)] emissions under oil contamination, we used functional gene array (GeoChip 5.0) analysis and network methods to investigate the feedback responses of soil microbial functional gene patterns and identify keystone genes in Shengli Oilfield, China. The microbial functional gene number, relative abundance and diversity involved in carbon degradation and nitrogen cycling decreased consistently with the reduced CO₂ and N₂O flux in oil contaminated soils, whereas the gene number and relative abundance of methane-production related genes increased with contamination. Functional molecular ecological networks were built based on random matrix theory, where network structures and properties showed significantly variation between oil contaminated and uncontaminated soils (P<0.05). Network nodes, connectivity and complexity all reduced under oil contamination. The sensitive and the highest connective genes in the network were identified as keystone genes, based on Mann-Whitney U tests and network analysis. Our findings improved the understanding of the microbe-mediated mechanisms affecting soil greenhouse gas emissions.

Microbial mechanisms of carbon priming effects revealed during the interaction of crop residue and nutrient inputs in contrasting soils

Agronomic practices such as crop residue return and additional nutrient supply are recommended to increase soil organic carbon (SOC) in arable farmlands. However, changes in the priming effect (PE) on native SOC mineralization in response to integrated inputs of residue and nutrients are not fully known. This knowledge gap along with a lack of understanding of microbial mechanisms hinders the ability to constrain models and to reduce the uncertainty to predict carbon (C) sequestration potential. Using a ¹³ C-labeled wheat residue, this 126-day incubation study examined the dominant microbial mechanisms that underpin the PE response to inputs of wheat residue and nutrients (nitrogen, phosphorus and sulfur) in two contrasting soils. The residue input caused positive PE through "co-metabolism," supported by increased microbial biomass, C and nitrogen (N) extracellular enzyme activities (EEAs), and gene abundance of certain microbial taxa (Eubacteria, β-Proteobacteria, Acidobacteria, and Fungi). The residue input could have induced nutrient limitation, causing an increase in the PE via "microbial nutrient mining" of native soil organic matter, as suggested by the low C-to-nutrient stoichiometry of EEAs. At the high residue, exogenous nutrient supply (cf. no-nutrient) initially decreased positive PE by alleviating nutrient mining, which was supported by the low gene abundance of Eubacteria and Fungi. However, after an initial decrease in PE at the high residue with nutrients, the PE increased to the same magnitude as without nutrients over time. This suggests the dominance of "microbial stoichiometry decomposition," supported by higher microbial biomass and EEAs, while Eubacteria and Fungi increased over time, at the high residue with nutrients cf. no-nutrient in both soils. Our study provides novel evidence that different microbial mechanisms operate simultaneously depending on organic C and nutrient availability in a residue-amended soil. Our results have consequences for SOC modeling and integrated nutrient management employed to increase SOC in arable farmlands.

Environmental factors shaping the diversity of bacterial communities that promote rice production

BACKGROUND

Exploiting soil microorganisms in the rhizosphere of plants can significantly improve agricultural productivity; however, the mechanism by which microorganisms specifically affect agricultural productivity is poorly understood. To clarify this uncertainly, the rhizospheric microbial communities of super rice plants at various growth stages were analysed using 16S rRNA high-throughput gene sequencing; microbial communities were then related to soil properties and rice productivity.

RESULTS

The rhizospheric bacterial communities were characterized by the phyla Proteobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia during all stages of rice growth. Rice production differed by approximately 30% between high- and low-yield sites that had uniform fertilization regimes and climatic conditions, suggesting the key role of microbial communities. Mantel tests showed a strong correlation between soil conditions and rhizospheric bacterial communities, and microorganisms had different effects on crop yield. Among the four growing periods, the rhizospheric bacterial communities present during the heading stage showed a more significant correlation (p <  0.05) with crop yield, suggesting their potential in regulating crop production. The biological properties (i.e., microbes) reflected the situation of agricultural land better than the physicochemical characterics (i.e., nutrient elements), which provides theoretical support for agronomic production. Molecular ecological network (MEN) analysis suggested that differences in productivity were caused by the interaction between the soil characteristics and the bacterial communities.

CONCLUSIONS

During the heading stage of rice cropping, the rhizospheric microbial community is vital for the resulting rice yield. According to network analysis, the cooperative relationship (i.e., positive interaction) between between microbes may contribute significantly to yield, and the biological properties (i.e., microbes) better reflected the real conditions of agricultural land than did the physicochemical characteristics (i.e., nutrient elements).

Apportioning bacterial carbon source utilization in soil using 14 C isotope analysis of FISH-targeted bacterial populations sorted by fluorescence activated cell sorting (FACS): 14 C-FISH-FACS

An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon-labelled substrate tracing, fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity (¹⁴ C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas spp. (and some Burkholderia spp.) and salicylic acid added to rhizosphere soil. We examined salicylic acid-¹⁴ C fate (mineralized, cell-incorporated, extractable and non-extractable) and mass balance (0-24 h) and show that the PSE1284 population captured ∼ 50% of the Nycodenz extracted biomass ¹⁴ C. Analysis of the taxonomic distribution of the salicylic acid biodegradation trait suggested that PSE1284 population success was not due to conservation of this trait but due to competitiveness for the added carbon. Adding 50KBq of ¹⁴ C sample^-1 enabled detection of ¹⁴ C in the sorted population at ∼ 60-600 times background; a sensitivity which demonstrates potential extension to analysis of rarer/less active populations. Given its sensitivity and compatibility with obtaining a C mass balance, ¹⁴ C-FISH-FACS allows quantitative dissection of C flow within the microbial biomass that has hitherto not been achieved.

Ecological patterns and adaptability of bacterial communities in alkaline copper mine drainage

Environmental gradient have strong effects on community assembly processes. In order to reveal the effects of alkaline mine drainage (AlkMD) on bacterial and denitrifying bacterial community compositions and diversity in tailings reservoir, here we conducted an experiment to examine all and core bacterial taxa and denitrifying functional genes's (nirS, nirK, nosZ_Ι) abundance along a chemical gradient in tailings water in Shibahe copper tailings in Zhongtiaoshan, China. Differences in bacterial and denitrifying bacterial community compositions in different habitats and their relationships with environmental parameters were analyzed. The results showed that the richness and diversity of bacterial community in downstream seeping water (SDSW) were the largest, while that in upstream tailings water (STW1) were the lowest. The diversity and abundance of bacterial communities tended to increase from STW1 to SDSW. The variation of bacterial community diversity was significantly related to electroconductibility (EC), nitrate (NO₃^-), nitrite (NO₂^-), total carbon (TC), inorganic carbon (IC) and sulfate (SO₄^2-), but was not correlated with geographic distance in local scale. Core taxa from class to genus were all significantly related to NO₃^- and NO₂^-. Core taxa Rhodobacteraceae, Rhodobacter, Acinetobacter and Hydrogenophaga were typical denitrifying bacteria. The variation trends of these groups were consistent with the copy number of nirS, nirK and nosZ_Ι, demonstrating their importance in the process of nitrogen reduction. The copy number of nirK, nosZ_Ι and nirS/16S rDNA, nirK/16Sr DNA correlated strongly with NO₃^-, NO₂^- and IC, but nirS and nosZ_I/16SrDNA had no significant correlation with NO₃^- and NO₂^-. The copy numbers of denitrifying functional genes (nirS, nirK and nosZ_Ι) were negatively correlated with heavy metal plumbum (Pb) and zinc (Zn). It showed that heavy metal contamination was an important factor affecting the structure of denitrifying bacterial community in AlkMD. In this study we have identified the distribution pattern of bacterial community along physiochemical gradients in alkaline tailings reservoir and displayed the driving force of shaping the structure of bacterial community. The influence of NO₃^-, NO₂^-, IC and heavy metal Pb and Zn on bacterial community might via their influence on the functional groups involving nitrogen, carbon and metal metabolisms.

Enhanced growth of halophyte plants in biochar-amended coastal soil: roles of nutrient availability and rhizosphere microbial modulation

Soil health is essential and irreplaceable for plant growth and global food production, which has been threatened by climate change and soil degradation. Degraded coastal soils are urgently required to reclaim using new sustainable technologies. Interest in applying biochar to improve soil health and promote crop yield has rapidly increased because of its multiple benefits. However, effects of biochar addition on the saline-sodic coastal soil health and halophyte growth were poorly understood. Response of two halophytes, Sesbania (Sesbania cannabina) and Seashore mallow (Kosteletzkya virginica), to the individual or co-application of biochar and inorganic fertilizer into a coastal soil was investigated using a 52 d pot experiment. The biochar alone or co-application stimulated the plant growth (germination, root development, and biomass), primarily attributed to the enhanced nutrient availability from the biochar-improved soil health. Additionally, the promoted microbial activities and bacterial community shift towards the beneficial taxa (e.g. Pseudomonas and Bacillus) in the rhizosphere also contributed to the enhanced plant growth and biomass. Our findings showed the promising significance because biochar added at an optimal level (≤5%) could be a feasible option to reclaim the degraded coastal soil, enhance plant growth and production, and increase soil health and food security.

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling

Forest soils represent important terrestrial carbon (C) pools where C is primarily fixed in the plant-derived biomass but it flows further through the biomass of fungi and bacteria before it is lost from the ecosystem as CO₂ or immobilized in recalcitrant organic matter. Microorganisms are the main drivers of C flow in forests and play critical roles in the C balance through the decomposition of dead biomass of different origins. Here, we track the path of C that enters forest soil by following respiration, microbial biomass production, and C accumulation by individual microbial taxa in soil microcosms upon the addition of ¹³C-labeled biomass of plant, fungal, and bacterial origin. We demonstrate that both fungi and bacteria are involved in the assimilation and mineralization of C from the major complex sources existing in soil. Decomposer fungi are, however, better suited to utilize plant biomass compounds, whereas the ability to utilize fungal and bacterial biomass is more frequent among bacteria. Due to the ability of microorganisms to recycle microbial biomass, we suggest that the decomposer food web in forest soil displays a network structure with loops between and within individual pools. These results question the present paradigms describing food webs as hierarchical structures with unidirectional flow of C and assumptions about the dominance of fungi in the decomposition of complex organic matter.

Impact of fomesafen on the soil microbial communities in soybean fields in Northeastern China

Fomesafen, a widely adopted residual herbicide, is used throughout the soybean region of northern China for the spring planting. However, the ecological risks of using fomesafen in soil remain unknown. The aim of this work was to evaluate the impact of fomesafen on the microbial community structure of soil using laboratory and field experiments. Under laboratory conditions, the application of fomesafen at concentrations of 3.75 and 37.5mg/kg decreased the basal respiration (RB) and microbial biomass carbon (MBC). In contrast, treatment with 375mg/kg of fomesafen resulted in a significant decrease in the RB, MBC, abundance of both Gram+ and Gram- bacteria, and fungal biomass. Analysis of variance showed that the treatment accounted for most of the variance (38.3%) observed in the soil microbial communities. Furthermore, the field experiment showed that long-term fomesafen application in continuously cropped soybean fields affected the soil bacterial community composition by increasing the relative average abundance of Proteobacteria and Actinobacteria species and decreasing the abundance of Verrucomicrobia species. In addition, Acidobacteria and Chloroflexi species showed a pattern of activation-inhibition. Taken together, our results suggest that the application of fomesafen can affect the community structure of soil bacteria in the spring planting soybean region of northern China.

Biochar-induced negative carbon mineralization priming effects in a coastal wetland soil: Roles of soil aggregation and microbial modulation

Biochar can sequestrate carbon (C) in soils and affect native soil organic carbon (SOC) mineralization via priming effects. However, the roles of soil aggregation and microbial regulation in priming effects of biochars on SOC in coastal wetland soils are poorly understood. Thus, a coastal wetland soil (δ¹³C -22‰) was separated into macro-micro aggregates (53-2000μm, MA) and silt-clay fractions (<53μm, SF) to investigate the priming effect using two ¹³C enriched biochars produced from corn straw (δ¹³C -11.58‰) at 350 and 550°C. The two biochars induced negative priming effect on the native SOC mineralization in the both soil aggregate size fractions, attributed to the enhanced stability of the soil aggregates resulting from the intimate physico-chemical associations between the soil minerals and biochar particles. Additionally, biochar amendments increased soil microbial biomass C and resulted in a lower metabolic quotient, suggesting that microbes in biochar amended aggregates could likely incorporate biomass C rather than mineralize it. Moreover, the biochar amendments induced obvious shifts of the bacterial community towards low C turnover bacteria taxa (e.g., Actinobacteria and Deltaproteobacteria) and the bacteria taxa responsible for stabilizing soil aggregates (e.g., Actinobacteria and Acidobacteria), which also accounted for the negative priming effect. Overall, these results suggested that biochar had considerable merit for stabilizing SOC in the coastal soil and thus has potential to restore and/or enhance "blue C" sink in the degraded coastal wetland ecosystem.

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting-drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide.

From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality

Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.