Nutrient availability greatly regulates soil microbial processes and functions in tropical forests. However, few studies have explored the impacts of nitrogen (N) addition (100 kg P ha⁻¹ year⁻¹), ...phosphorus (P) addition (100 kg N ha⁻¹ year⁻¹), and N × P interaction on soil microbial biomass and microbial community composition in tropical forests. We established a field nutrient manipulation experiment in a secondary tropical forest of South China. Soil physicochemical properties and microbial community composition were measured. Analysis of phospholipid fatty acids (PLFAs) was used to determine soil microbial biomass and composition, and both were related to environmental factors by the redundancy analysis (RDA) and principal response curves (PRC). We demonstrated that N addition usually did not affect microbial biomass, which was increased by P addition over 3 years of fertilization. Nitrogen addition decreased soil bacterial biomass but did not affect soil fungal biomass after 3 years of fertilization. After P addition, soil fungal biomass increased faster than soil bacterial biomass, indicating a more sensitive response of soil fungi to P addition than bacteria. Phosphorus addition increased fungi/bacteria ratio (F/B) ratios after 3 years of fertilization. Both N and P additions had different effects on soil microbial community in this tropical forest and, thus, probably altered ecosystem functioning.
To optimally employ Natural Source Zone Depletion (NSZD) and Enhanced Source Zone Depletion (ESZD) at sites impacted by light non-aqueous phase liquids (LNAPL), monitoring strategies are required. ...Emerging use of subsurface oxidation-reduction potential (ORP) sensors shows promise for tracking redox evolution, which reflects ongoing biogeochemical processes. However, further understanding of how soil redox dynamics relate to subsurface microbial activity and LNAPL degradation pathways is needed. In this work, soil ORP sensors and DNA and RNA sequencing-based microbiome analysis were combined to elucidate NSZD and ESZD (biostimulation via periodic sulfate addition and biosparging) processes in columns containing LNAPL-impacted soils from a former petroleum refinery. Results show expected relationships between continuous soil redox and active microbial communities. Continuous data revealed spatial and temporal detail that informed interpretation of the hydrocarbon biodegradation data. Redox increases were transient for sulfate addition, and sequencing revealed how hydrocarbon concentration and composition impacted microbiome structure and naphthalene degradation. Periodic biosparging did not result in fully aerobic conditions suggesting observed biodegradation improvements could be explained by alternative anaerobic metabolisms (e.g., iron reduction due to air oxidizing reduced iron). Collectively, data suggest combining continuous redox sensing with microbiome analysis provides insights beyond those possible with either monitoring tool alone.
Subsurface light non-aqueous phase liquids (LNAPL) pose human health and environmental risks. Thus, there is a need to develop remediation technologies to address LNAPL source zones, including Natural Source Zone Depletion (NSZD) and Enhanced Source Zone Depletion (ESZD). Sulfate addition and biosparging are promising ESZD technologies. To monitor remediation progress, guide decision-making regarding implementation, and support regulatory approval, in situ monitoring tools are desired. Use of continuous soil redox sensors, combined with next-generation sequencing of cryogenically preserved soil to characterize total and active subsurface microbiomes, provided critical insights regarding evolving biogeochemical processes during NSZD, period sulfate addition, and biosparging.
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•Redox dynamics and active microbiomes investigated during natural source zone depletion (NSZD) and enhanced SZD.•Continuous ORP data resolves distinct spatial/temporal patterns impacting biodegradation performance.•ORP measurements consistent with active microbiome structure data.•Differences in LNAPL composition affect naphthalene degradation mechanism.•Active Smithella spp. prevalent in alkane rich environments.
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•Microbiota are important for plant growth, health and stress resilience.•Inoculation with key microbiota members can improve plant traits.•Tailored selection and delivery of ...microbial strains or consortia is required.•Microbiome improvement may be achieved by appropriate agro-management practices.•Plant breeding for improved interaction with microbiota will be of benefit.
Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount of information is now available on the structure and dynamics of plant microbiota as well as on the functional capacities of isolated community members. Due to the interesting functional potential of plant microbiota as well as due to current challenges in crop production there is an urgent need to bring microbial innovations into practice. Different approaches for microbiome improvement exist. On the one hand microbial strains or strain combinations can be applied, however, field success is often variable and improvement is urgently required. Smart, knowledge-driven selection of microorganisms is needed as well as the use of suitable delivery approaches and formulations. On the other hand, farming practices or the plant genotype can influence plant microbiota and thus functioning. Therefore, selection of appropriate farming practices and plant breeding leading to improved plant-microbiome interactions are avenues to increase the benefit of plant microbiota. In conclusion, different avenues making use of a new generation of inoculants as well as the application of microbiome-based agro-management practices and improved plant lines could lead to a better use of the plant microbiome. This paper reviews the importance and functionalities of the bacterial plant microbiome and discusses challenges and concepts in regard to the application of plant-associated bacteria.
The Park Grass experiment (PGE) in the UK has been ongoing since 1856. Its purpose is to study the response of biological communities to the long-term treatments and associated changes in soil ...parameters, particularly soil pH. In this study, soil samples were collected across pH gradient (pH 3.6–7) and a range of fertilizers (nitrogen as ammonium sulfate, nitrogen as sodium nitrate, phosphorous) to evaluate the effects nutrients have on soil parameters and microbial community structure. Illumina 16S ribosomal RNA (rRNA) amplicon sequencing was used to determine the relative abundances and diversity of bacterial and archaeal taxa. Relationships between treatments, measured soil parameters, and microbial communities were evaluated. Clostridium, Bacteroides, Bradyrhizobium, Mycobacterium, Ruminococcus, Paenibacillus, and Rhodoplanes were the most abundant genera found at the PGE. The main soil parameter that determined microbial composition, diversity, and biomass in the PGE soil was pH. The most probable mechanism of the pH impact on microbial community may include mediation of nutrient availability in the soil. Addition of nitrogen to the PGE plots as ammonium sulfate decreases soil pH through increased nitrification, which causes buildup of soil carbon, and hence increases C/N ratio. Plant species richness and plant productivity did not reveal significant relationships with microbial diversity; however, plant species richness was positively correlated with soil microbial biomass. Plants responded to the nitrogen treatments with an increase in productivity and a decrease in the species richness.
Roots of healthy plants are inhabited by soil-derived bacteria, fungi, and oomycetes that have evolved independently in distinct kingdoms of life. How these microorganisms interact and to what extent ...those interactions affect plant health are poorly understood. We examined root-associated microbial communities from three Arabidopsis thaliana populations and detected mostly negative correlations between bacteria and filamentous microbial eukaryotes. We established microbial culture collections for reconstitution experiments using germ-free A. thaliana. In plants inoculated with mono- or multi-kingdom synthetic microbial consortia, we observed a profound impact of the bacterial root microbiota on fungal and oomycetal community structure and diversity. We demonstrate that the bacterial microbiota is essential for plant survival and protection against root-derived filamentous eukaryotes. Deconvolution of 2,862 binary bacterial-fungal interactions ex situ, combined with community perturbation experiments in planta, indicate that biocontrol activity of bacterial root commensals is a redundant trait that maintains microbial interkingdom balance for plant health.
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•Roots of healthy plants are colonized by multi-kingdom microbial consortia•Bacterial Root Commensals (BRCs) shape fungal and oomycetal community structure•BRCs protect plants against fungi and oomycetes•Biocontrol activity of BRCs is a redundant trait and essential for plant survival
An interkingdom analysis of the microbes associated with Arabidopsis roots explains their functional contributions to plant survival.
Biochar has received extensive attention because of its multi-functionality for agricultural and environmental applications. Despite its many benefits, there are concerns related to the long-term ...safety and implications of its application, mainly because the mechanisms affecting soil and organism health are poorly quantified and understood. This work reviews 259 sources and summarises existing knowledge on biochar's adverse effects on soil from a multiangle perspective, including the physicochemical changes in soil, reduced efficiency of agrochemicals, potentially toxic substances in biochar, and effects on soil biota. Suggestions are made for mitigation measures. Mixed findings are often reported; however, the results suggest that high doses of biochar in clay soils are likely to decrease available water content, and surface application of biochar to sandy soils likely increases erosion and particulate matter emissions. Furthermore, biochar may increase the likelihood of excessive soil salinity and decreased soil fertility because of an increase in the pH of alkaline soils causing nutrient precipitation. Regarding the impact of biochar on (agro)chemicals and the role of biochar-borne toxic substances, these factors cannot be neglected because of their apparent undesirable effects on target and non-target organisms, respectively. Concerning non-target biota, adverse effects on reproduction, growth, and DNA integrity of earthworms have been reported along with effects on soil microbiome such as a shift in the fungi-to-bacteria ratio. Given the diversity of effects that biochar may induce in soil, guidelines for future biochar use should adopt a structured and holistic approach that considers all positive and negative effects of biochar.
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•The review summarises the possible adverse biochar effects considering 259 studies.•Adverse effects may arise due to changes in soil properties upon biochar addition.•Soil organisms, mostly earthworms, suffer from biological adverse effects of biochar.•Several unfavourable soil-biochar combinations were identified.•A holistic approach is needed to reveal all possible, long-term adverse effects.
Under the current paradigm, organic matter decomposition and nutrient cycling rates are a function of the imbalance between substrate and microbial biomass stoichiometry. Challenging this view, we ...demonstrate that in an individual‐based model, microbial community dynamics alter relative C and N limitation during litter decomposition, leading to a system behaviour not predictable from stoichiometric theory alone. Rather, the dynamics of interacting functional groups lead to an adaptation at the community level, which accelerates nitrogen recycling in litter with high initial C : N ratios and thus alleviates microbial N limitation. This mechanism allows microbial decomposers to overcome large imbalances between resource and biomass stoichiometry without the need to decrease carbon use efficiency (CUE), which is in contrast to predictions of traditional stoichiometric mass balance equations. We conclude that identifying and implementing microbial community‐driven mechanisms in biogeochemical models are necessary for accurately predicting terrestrial C fluxes in response to changing environmental conditions.
•Microbial community of 18 food waste anaerobic digesters (AD) was characterised.•Temperature was one of the strongest drivers of microbial community structure.•Methanogens were influenced by a ...complex combination of operational conditions.•Food waste may promote AD robustness with diverse syntrophic microbes.•Potential usage of microbial data in food waste AD management is discussed.
Anaerobic digestion of food waste is an attractive and increasingly popular technology within waste management and energy recovery. A better understanding of the microbiology associated with anaerobic digestion of food waste will provide new insight into the operational conditions required for optimizing this process, as well as its potential for utilisation in co-digestion systems. Eighteen full-scale reactors processing varying proportions of food waste under diverse operational configurations were subjected to microbial community analysis by amplicon sequencing of the 16S rRNA and mcrA genes to capture the bacterial and methanogenic populations. Statistical correlations between microbial populations, plant design and operating conditions revealed that the microbial communities were shaped by operational parameters such as the primary substrate type and operational temperature, while the methanogenic communities showed a more reactor specific distribution. The distribution of microbes based on the waste processed in the surveyed digesters was explored, as well as the presence of specialist populations such as syntrophs and methanogens. Food waste digester communities were not associated with a strong microbial fingerprint compared to other waste types (wastewater and manure) but contained greater abundance and unique syntrophic acetate oxidising populations, suggesting that co-digestion with food waste may improve the functional diversity of anaerobic digesters.
Microorganisms can attach on the surface of microplastics (MPs) through biological fouling process to form a diverse community called the "plastisphere", which has attracted extensive attention. ...Although the microbial structure and composition of biofilm have been studied, the knowledge of its microbial function and ecological risk is still limited. In this study, we investigated how the surface properties of MPs affect the biofilm communities and metabolic features under different environmental conditions, and explored the biofilm enrichment of antibiotic resistance genes (ARGs). The results showed that the incubation time, habitat and MPs aging state significantly influenced the structure and composition of biofilm microbial communities, and a small amount of pathogens have been found in the MPs-attached biofilm. The microbial carbon utilization capacity of the biofilm in different incubation habitats varies greatly with highest metabolism capacity appear in the river. The utilization efficiency of different carbon sources is polymer > carbohydrate > amino acid > carboxylic acids > amine/amide, which indicates that the biofilm communities have selectivity between different types of carbon sources. More importantly, ARGs were detected in all the MPs samples and showed a trend of estuary > river > marine. The aged MPs can accumulate more ARGs than the virgin items. In general, MPs in the aquatic environment may become a carrier for pathogens and ARGs to spread to other environment, which may enhance their potential risks to the ecosystem and human health.
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•The composition and abundance of plastisphere are affected by environmental factors.•Microbial communities in river habitat have high carbon utilization capacity.•Plastisphere may affect microbial mediated carbon cycle in aquatic environment.•Antibiotic resistance genes enriched on the aged microplastics.
This study was carried out to understand microbial diversity and function in the microbial enhanced oil recovery (MEOR) process and to assess the impact of MEOR treatment on the microbial community ...in an oil reservoir. The Illumina MiSeq-based method was used to investigate the structure and dynamics of the microbial community in a MEOR-treated block of the Baolige oilfield, China. The results showed that microbial diversity was high and that 23 phyla occurred in the analyzed samples. Proteobacteria, Firmicutes, Bacteroidetes, Thermotogae, and Euryarchaeota were present in relatively high abundance in all analyzed samples. Injection of bacteria and nutrients resulted in interesting changes in the composition of the microbial community. During MEOR treatment, the community was dominated by the known hydrocarbon-utilizing genera Pseudomonas and Acinetobacter. After the treatment, the two genera decreased in abundance over time while Methanobacteriaceae, as well as known syntrophic genera such as Syntrophomonas, Pelotomaculum, Desulfotomaculum, and Thermacetogenium gradually increased. The change in dominant microbial populations indicated the presence of a succession of microbial communities over time, and the hydrocarbon degradation and syntrophic oxidation of acetate and propionate to methane in the MEOR-treated oilfield. This work contributes to a better understanding of microbial processes in oil reservoirs and helps to optimize MEOR technology.
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