Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO₂

Rhizosphere engineering for soil carbon sequestration

The rhizosphere is the central hotspot of water and nutrient uptake by plants, rhizodeposition, microbial activities, and plant-soil-microbial interactions. The plasticity of plants offers possibilities to engineer the rhizosphere to mitigate climate change. We define rhizosphere engineering as targeted manipulation of plants, soil, microorganisms, and management to shift rhizosphere processes for specific aims [e.g., carbon (C) sequestration]. The rhizosphere components can be engineered by agronomic, physical, chemical, biological, and genomic approaches. These approaches increase plant productivity with a special focus on C inputs belowground, increase microbial necromass production, protect organic compounds and necromass by aggregation, and decrease C losses. Finally, we outline multifunctional options for rhizosphere engineering: how to boost C sequestration, increase soil health, and mitigate global change effects.

Role of Arbuscular Mycorrhizal Fungi in Regulating Growth, Enhancing Productivity, and Potentially Influencing Ecosystems under Abiotic and Biotic Stresses

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with the roots of nearly all land-dwelling plants, increasing growth and productivity, especially during abiotic stress. AMF improves plant development by improving nutrient acquisition, such as phosphorus, water, and mineral uptake. AMF improves plant tolerance and resilience to abiotic stressors such as drought, salt, and heavy metal toxicity. These benefits come from the arbuscular mycorrhizal interface, which lets fungal and plant partners exchange nutrients, signalling molecules, and protective chemical compounds. Plants' antioxidant defence systems, osmotic adjustment, and hormone regulation are also affected by AMF infestation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress conditions. As a result of its positive effects on soil structure, nutrient cycling, and carbon sequestration, AMF contributes to the maintenance of resilient ecosystems. The effects of AMFs on plant growth and ecological stability are species- and environment-specific. AMF's growth-regulating, productivity-enhancing role in abiotic stress alleviation under abiotic stress is reviewed. More research is needed to understand the molecular mechanisms that drive AMF-plant interactions and their responses to abiotic stresses. AMF triggers plants' morphological, physiological, and molecular responses to abiotic stress. Water and nutrient acquisition, plant development, and abiotic stress tolerance are improved by arbuscular mycorrhizal symbiosis. In plants, AMF colonization modulates antioxidant defense mechanisms, osmotic adjustment, and hormonal regulation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress circumstances. AMF-mediated effects are also enhanced by essential oils (EOs), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), hydrogen peroxide (H2O2), malondialdehyde (MDA), and phosphorus (P). Understanding how AMF increases plant adaptation and reduces abiotic stress will help sustain agriculture, ecosystem management, and climate change mitigation. Arbuscular mycorrhizal fungi (AMF) have gained prominence in agriculture due to their multifaceted roles in promoting plant health and productivity. This review delves into how AMF influences plant growth and nutrient absorption, especially under challenging environmental conditions. We further explore the extent to which AMF bolsters plant resilience and growth during stress.

Plant -microbe assisted emerging contaminants (ECs) removal and carbon cycling

Continuous increase in the level of atmospheric CO₂ and environmental contaminates has aggravated various threats resulting from environmental pollution and climate change. Research into plant -microbe interaction has been a central concern of ecology for over the year. However, despite the clear contribution of plant -microbe to the global carbon cycle, the role of plant -microbe interaction in carbon pools, fluxes and emerging contaminants (ECs) removal are still a poorly understood. The use of plant and microbes in ECs removal and carbon cycling is an attractive strategy because microbes operate as biocatalysts to remove contaminants and plant roots offer a rich niche for their growth and carbon cycling. However, bio-mitigation of CO₂ and removal of ECs is still under research phase because of the CO₂ capture and fixation efficiency is too low for industrial purposes and cutting-edge removal methods have not been created for such emerging contaminants.

Environmental microbiome engineering for the mitigation of climate change

Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables

Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and bla_TEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.

Responses of the Mushroom Pleurotus ostreatus under Different CO2 Concentration by Comparative Proteomic Analyses

BACKGROUND

Pleurotus ostreatus is a popular edible mushroom in East Asian markets. Research on the responses of P. ostreatus under different carbon dioxide concentrations is limited.

METHODS

Label-free LC-MS/MS quantitative proteomics analysis technique was adopted to obtain the protein expression profiles of P. ostreatus fruiting body pileus collected under different carbon dioxide concentrations. The Pearson correlation coefficient analysis and principal component analysis were performed to reveal the correlation among samples. The differentially expressed proteins (DEPs) were organized. Gene ontology analysis was performed to divide the DEPs into different metabolic processes and pathways.

RESULTS

The expansion of stipes was inhibited in the high CO2 group compared with that in the low CO2 group. There were 415 DEPs (131 up- and 284 down-regulated) in P. ostreatus PH11 treated with 1% CO2 concentration compared with P. ostreatus under atmospheric conditions. Proteins related to hydrolase activity, including several amidohydrolases and cell wall synthesis proteins, were highly expressed under high CO2 concentration. Most of the kinases and elongation factors were significantly down-regulated under high CO2 concentration. The results suggest that the metabolic regulation and development processes were inhibited under high CO2 concentrations. In addition, the sexual differentiation process protein Isp4 was inhibited under high CO2 concentrations, indicating that the sexual reproductive process was also inhibited under high CO2 concentrations, which is inconsistent with the small fruiting body pileus under high CO2 concentrations.

CONCLUSIONS

This research reports the proteome analysis of commercially relevant edible fungi P. ostreatus under different carbon dioxide concentrations. This study deepens our understanding of the mechanism for CO2-induced morphological change in the P. ostreatus fruiting body, which will facilitate the artificial cultivation of edible mushrooms.

Multifarious Responses of Forest Soil Microbial Community Toward Climate Change

Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO₂, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.

The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria

Background

The 'Microphenotron' is an automated screening platform that uses 96-well microtiter plates to test the response of seedlings to natural products. This system allows monitoring the phenotypic effect of a large number of small molecules. Here, this model system was used to study the effect of phytohormones produced by plant growth-promoting rhizobacteria (PGPR) on the growth of wild-type and mutant lines of Arabidopsis thaliana.

Methods

In the present study, high-throughput screening based on 'Microphenotron' was used to screen PGPRs. Rhizobacteria were isolated from the rhizosphere of Acacia Arabica, which was growing in saline habitats. The phylogeny of these rhizobacteria was determined by 16S rRNA gene sequencing. Strains were screened for plant growth-promoting traits such as auxin production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization. Ultra-Performance Liquid Chromatography (UPLC) was used to detect the presence of different indolic compounds. Finally, PGPR were evaluated to enhance the growth of A. thaliana in the 'Microphenotron' system and pot trials.

Results

Selected rhizobacteria strains showed positive results for multiple plant-growth promoting traits. For instance, strain (S-6) of Bacillus endophyticus exhibited the highest ACC-deaminase activity. UPLC analysis indicated the presence of different indolic compounds in bacterial extracts that included indole lactic acid (ILA), indole carboxylic acid (ICA), and indole-3-acetic acid (IAA). Two strains (S-7 and S-11) of Psychrobacter alimentarius produced the most IAA, ICA and ILA. A screening bioassay through 96-well microtiter plates with wild-type Col. N6000 showed an increase in root growth and proliferation. The highest twofold increase was recorded in root growth with B. thuringiensis S-26 and B. thuringiensis S-50. In pot trials, mutant lines of A. thaliana impaired for auxin signaling showed that B. endophyticus S-6, Psy. alimenterius S-11, Enterobacter asburiae S-24 and B. thuringiensis S-26 used auxin signaling for plant growth promotion. Similarly, for ethylene insensitive mutant lines (ein2.5 and etr1), Prolinoborus fasciculus S-3, B. endophyticus S-6, Psy. alimenterius S-7, E. asburiae S-24, and B. thuringiensis S-26 showed the involvement of ethylene signaling. However, the growth promotion pattern for most of the strains indicated the involvement of other mechanisms in enhancing plant growth. The result of Microphenotron assays generally agreed with pot trials with mutant and wild type A. thaliana varieties. Bacterial strains that induced the highest growth response by these cultivars in the 'Microphenotron' promoted plant growth in pot trials. This suggests that Microphenotron can accelerate the evaluation of PGPR for agricultural applications.

The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges

Microbial inoculations contribute to reducing agricultural systems' environmental footprint by supporting sustainable production and regulating climate change. However, the indirect and cascading effects of microbial inoculants through the reshaping of soil microbiome are largely overlooked. By discussing the underlying mechanisms of plant- and soil-based microbial inoculants, we suggest that a key challenge in microbial inoculation is to understand their legacy on indigenous microbial communities and the corresponding impacts on agroecosystem functions and services relevant to climate change. We explain how these legacy effects on the soil microbiome can be understood by building on the mechanisms driving microbial invasions and placing inoculation into the context of ecological succession and community assembly. Overall, we advocate that generalizing field trials to systematically test inoculants' effectiveness and developing knowledge anchored in the scientific field of biological/microbial invasion are two essential requirements for applying microbial inoculants in agricultural ecosystems to tackle climate change challenges.

Growth and Nutritional Quality of Lemnaceae Viewed Comparatively in an Ecological and Evolutionary Context

This review focuses on recently characterized traits of the aquatic floating plant Lemna with an emphasis on its capacity to combine rapid growth with the accumulation of high levels of the essential human micronutrient zeaxanthin due to an unusual pigment composition not seen in other fast-growing plants. In addition, Lemna's response to elevated CO₂ was evaluated in the context of the source-sink balance between plant sugar production and consumption. These and other traits of Lemnaceae are compared with those of other floating aquatic plants as well as terrestrial plants adapted to different environments. It was concluded that the unique features of aquatic plants reflect adaptations to the freshwater environment, including rapid growth, high productivity, and exceptionally strong accumulation of high-quality vegetative storage protein and human antioxidant micronutrients. It was further concluded that the insensitivity of growth rate to environmental conditions and plant source-sink imbalance may allow duckweeds to take advantage of elevated atmospheric CO₂ levels via particularly strong stimulation of biomass production and only minor declines in the growth of new tissue. It is proposed that declines in nutritional quality under elevated CO₂ (due to regulatory adjustments in photosynthetic metabolism) may be mitigated by plant-microbe interaction, for which duckweeds have a high propensity.

Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces

In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a ¹³CO₂ atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several ¹³C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily ¹³C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil.

IMPORTANCE Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO₂-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.

Temperature effect on water dynamics in tetramer phosphofructokinase matrix and the super-arrhenius respiration rate

Advances in understanding the temperature effect on water dynamics in cellular respiration are important for the modeling of integrated energy processes and metabolic rates. For more than half a century, experimental studies have contributed to the understanding of the catalytic role of water in respiration combustion, yet the detailed water dynamics remains elusive. We combine a super-Arrhenius model that links the temperature-dependent exponential growth rate of a population of plant cells to respiration, and an experiment on isotope labeled ¹⁸O₂ uptake to H₂¹⁸O transport role and to a rate-limiting step of cellular respiration. We use Phosphofructokinase (PFK-1) as a prototype because this enzyme is known to be a pacemaker (a rate-limiting enzyme) in the glycolysis process of respiration. The characterization shows that PFK-1 water matrix dynamics are crucial for examining how respiration (PFK-1 tetramer complex breathing) rates respond to temperature change through a water and nano-channel network created by the enzyme folding surfaces, at both short and long (evolutionary) timescales. We not only reveal the nano-channel water network of PFK-1 tetramer hydration topography but also clarify how temperature drives the underlying respiration rates by mapping the channels of water diffusion with distinct dynamics in space and time. The results show that the PFK-1 assembly tetramer possesses a sustainable capacity in the regulation of the water network toward metabolic rates. The implications and limitations of the reciprocal-activation-reciprocal-temperature relationship for interpreting PFK-1 tetramer mechanisms are briefly discussed.

PGPR Mediated Alterations in Root Traits: Way Toward Sustainable Crop Production

The above ground growth of the plant is highly dependent on the belowground root system. Rhizosphere is the zone of continuous interplay between plant roots and soil microbial communities. Plants, through root exudates, attract rhizosphere microorganisms to colonize the root surface and internal tissues. Many of these microorganisms known as plant growth promoting rhizobacteria (PGPR) improve plant growth through several direct and indirect mechanisms including biological nitrogen fixation, nutrient solubilization, and disease-control. Many PGPR, by producing phytohormones, volatile organic compounds, and secondary metabolites play important role in influencing the root architecture and growth, resulting in increased surface area for nutrient exchange and other rhizosphere effects. PGPR also improve resource use efficiency of the root system by improving the root system functioning at physiological levels. PGPR mediated root trait alterations can contribute to agroecosystem through improving crop stand, resource use efficiency, stress tolerance, soil structure etc. Thus, PGPR capable of modulating root traits can play important role in agricultural sustainability and root traits can be used as a primary criterion for the selection of potential PGPR strains. Available PGPR studies emphasize root morphological and physiological traits to assess the effect of PGPR. However, these traits can be influenced by various external factors and may give varying results. Therefore, it is important to understand the pathways and genes involved in plant root traits and the microbial signals/metabolites that can intercept and/or intersect these pathways for modulating root traits. The use of advanced tools and technologies can help to decipher the mechanisms involved in PGPR mediated determinants affecting the root traits. Further identification of PGPR based determinants/signaling molecules capable of regulating root trait genes and pathways can open up new avenues in PGPR research. The present review updates recent knowledge on the PGPR influence on root architecture and root functional traits and its benefits to the agro-ecosystem. Efforts have been made to understand the bacterial signals/determinants that can play regulatory role in the expression of root traits and their prospects in sustainable agriculture. The review will be helpful in providing future directions to the researchers working on PGPR and root system functioning.

Role of Epichloë Endophytes in Improving Host Grass Resistance Ability and Soil Properties

The past decade has witnessed significant advances in understanding the interaction between grasses and systemic fungal endophytes of the genus Epichloë, with evidence that plants have evolved multiple strategies to cope with abiotic stresses by reprogramming physiological responses. Soil nutrients directly affect plant growth, while soil microbes are also closely connected to plant growth and health. Epichloë endophytes could affect soil fertility by modifying soil nutrient contents and soil microbial diversity. Therefore, we analyze recent advances in our understanding of the role of Epichloë endophytes under the various abiotic stresses and the role of grass-Epichloë symbiosis on soil fertility. Various cool-season grasses are infected by Epichloë species, which contribute to health, growth, persistence, and seed survival of host grasses by regulating key systems, including photosynthesis, osmotic regulation, and antioxidants and activity of key enzymes of host physiology processes under abiotic stresses. The Epichloë endophyte offers significant prospects to magnify the crop yield, plant resistance, and food safety in ecological systems by modulating soil physiochemical properties and soil microbes. The enhancing resistance of host grasses to abiotic stresses by an Epichloë endophyte is a complex manifestation of different physiological and biochemical events through regulating soil properties and soil microbes by the fungal endophyte. The Epichloë-mediated mechanisms underlying regulation of abiotic stress responses are involved in osmotic adjustment, antioxidant machinery, photosynthetic system, and activity of key enzymes critical in developing plant adaptation strategies to abiotic stress. Therefore, the Epichloë endophytes are an attractive choice in increasing resistance of plants to abiotic stresses and are also a good candidate for improving soil fertility and regulating microbial diversity to improve plant growth.

Brown gold of marginal soil: Plant growth promoting bacteria to overcome plant abiotic stress for agriculture, biofuels and carbon sequestration

Marginal land is defined as land with poor soil characteristics and low crop productivity with no potential for profit. Poor soil quality due to the presence of xenobiotics or climate change is of great concern. Sustainable food production with increasing population is a challenge which becomes more difficult due to poor soil quality. Marginal soil can be made productive with the use of Plant Growth Promoting Bacteria (PGPB). This review outlines how PGPB can be used to improve marginal soil quality and its implications on agriculture, rhizoremediation, abiotic stress (drought, salinity and heavy metals) tolerance, carbon sequestration and production of biofuels. The feasibility of the idea is supported by several studies which showed maximal increase in the growth of plants inoculated with PGPB than to uninoculated plants grown in marginal soil when compared to the growth of plants inoculated with PGPB in healthy soil. The combination of PGPB and plants grown in marginal soil will serve as a green technology leading to the next green revolution, reduction in soil pollution and fossil fuel use, neutralizing abiotic stress and climate change effects.

Comparative Transcriptomics of Flammulina filiformis Suggests a High CO2 Concentration Inhibits Early Pileus Expansion by Decreasing Cell Division Control Pathways

Carbon dioxide is commonly used as one of the significant environmental factors to control pileus expansion during mushroom cultivation. However, the pileus expansion mechanism related to CO₂ is still unknown. In this study, the young fruiting bodies of a popular commercial mushroom Flammulina filiformis were cultivated under different CO₂ concentrations. In comparison to the low CO₂ concentration (0.05%), the pileus expansion rates were significantly lower under a high CO₂ concentration (5%). Transcriptome data showed that the up-regulated genes enriched in high CO₂ concentration treatments mainly associated with metabolism processes indicated that the cell metabolism processes were active under high CO₂ conditions. However, the gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with cell division processes contained down-regulated genes at both 12 h and 36 h under a high concentration of CO₂. Transcriptome and qRT-PCR analyses demonstrated that a high CO₂ concentration had an adverse effect on gene expression of the ubiquitin–proteasome system and cell cycle–yeast pathway, which may decrease the cell division ability and exhibit an inhibitory effect on early pileus expansion. Our research reveals the molecular mechanism of inhibition effects on early pileus expansion by elevated CO₂, which could provide a theoretical basis for a CO₂ management strategy in mushroom cultivation.

Plant functional diversity drives carbon storage following vegetation restoration in Loess Plateau, China

Ongoing climatic changes induced by human activities increases in atmospheric carbon dioxide (CO₂), which have considerable effects on the structure and function of ecosystems, including carbon (C) storage, plant functional traits and therefore on a wide set of ecosystem services. Plant functional diversity is benefit to improve plant photosynthesis and enhance C efficiency and therefore decrease CO₂. Here, the focus of this article is on integrating of plant functional diversity and C storage, which aims to contribute to C sequestration for climate change mitigation following vegetation restoration in Loess Plateau, China. Firstly, the CWM (plant community-weighted mean) traits of the most abundant plant species can account for C storage in AGBC (above-ground biomass C), ALC (above-ground litter C), STC (soil total carbon) and TEC (total ecosystem carbon). Secondly, the CWM of plant height and LCC (leaf carbon concentration) had a positive effect C storage in different part (AGBC, ALC, STC and TEC), while the CWM of LNC (leaf nitrogen concentration) and SLA (specific leaf area) had a negative effect on C storage in different part. Further, the CWM of plant height, LCC, SLA and plant functional dispersion (FDis) can be used to predict C storage by multiple linear regression analysis. Finally, the positive association between FDis and C storage was found in SEM, shedding light on the key role of plant functional diversity driving C storage following vegetation restoration. The findings presented here highlight the importance of both plant traits of dominant species and plant functional diversity in regulating C storage, and show that favorable climate conditions, particularly vegetation restoration, tend to increase C storage and plant functional diversity, which have important implications for improving global C cycling and ecosystem services.

Role of biochar and plant growth promoting rhizobacteria to enhance soil carbon sequestration-a review

Global climate is undergoing significant changes due to extensive release of greenhouse gases (GHGs) such as CO₂ and methane in the atmosphere. These gases are produced and released as a result of anthropogenic activities and fossil fuel burnings which also result in depletion of soil carbon resources. Biochar has various distinctive properties, which contribute to make it an effective, economical, and eco-friendly approach for soil carbon sequestration. The versatility in physicochemical properties of biochar provides an opportunity to optimize its efficacy to obtain desired benefits. A critical review of the literature indicates that biochar and plant growth-promoting microbes have the potential to improve soil organic carbon (SOC). Recent studies have depicted a significant role of the combined application of plant growth-promoting microbes and biochar on SOC dynamics. In future, these areas need to be explored as these have the potential to improve SOC dynamics and it could be a better strategy to sustain natural resources and ultimately mitigation of the climate change.

Susceptibility of soil organic carbon to priming after long-term CO2 fumigation is mediated by soil texture

Elevated CO₂ (eCO₂) may enhance soil organic carbon (SOC) sequestration via greater input of photosynthetic carbon (C). However, greater rhizodeposits under eCO₂ may stimulate microbial decomposition of native SOC. This study aimed to examine the status and stability of SOC in three Australian cropping soils after long-term CO₂ enrichment. Samples (0-5 cm) of Chromosol, Vertosol and Calcarosol soils were collected from an 8-year Free-air CO₂ Enrichment (SoilFACE) experiment and were used to examine SOC dynamics by physical fractionation and incubation with ¹³C-glucose. Compared to the ambient CO₂ (aCO₂) (390-400 μmol mol^-1), 8 years of elevated CO₂ (eCO₂) (550 μmol mol^-1) did not increase SOC concentration of all soils, but changed SOC distribution with 12% more C in coarse soil fractions and 5% less C in fine fractions. Elevated CO₂ also enhanced the susceptibility of SOC to ¹³C-glucose-induced priming, but this effect was only significant in the coarse-textured Calcarosol topsoil. The eCO₂ history increased labile C (coarse C fraction, +13%) and soil pH (+0.25 units), and decreased available N (-30%) in the Calcarosol, which stimulated microbial biomass C by 28%, leading to an enhanced priming effect. Despite with greater total primed C, the Chromosol that had the highest amount of native C, had lower primed C per unit of SOC when compared to the low-C Calcarosol. In conclusion, the effect of long-term eCO₂ enrichment on soil C and N availability in cropping soils depended on soil type with the coarse-textured Calcarosol soil being more susceptible to substrate-induced decomposition of its SOC.

Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates

Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. We employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates (ITC) obtained from rapeseed glucosinolates. Rapeseed-derived ITCs, including the cyclic, stable goitrin, are secondary metabolites with strong allelopathic affects against other plants, fungi and nematodes, and in addition can represent a health risk for human and animals. However, the effects of ITC application on the different bacterial and fungal organisms in soil are not known in detail. ITCs diminished the diversity of bacteria and fungi. After exposure, only few bacterial taxa of the Gammaproteobacteria, Bacteriodetes and Acidobacteria proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Many surviving microorganisms in ITC-treated soil where previously shown to harbor plant growth promoting properties. Cultivable fungi and bacteria were isolated from treated soils. A large number of cultivable microbial strains was capable of mobilizing soluble phosphate from insoluble calcium phosphate, and their application to Arabidopsis plants resulted in increased biomass production, thus revealing growth promoting activities. Therefore, inclusion of rapeseed-derived glucosinolates during biofumigation causes losses of microbiota, but also results in enrichment with ITC-tolerant plant microorganisms, a number of which show growth promoting activities, suggesting that Brassicaceae plants can shape soil microbiota community structure favoring bacteria and fungi beneficial for Brassica plants.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

Drought remains a critical obstacle to meeting the food demands of the coming century. Understanding the interplay between drought stress, plant development, and the plant microbiome is central to meeting this challenge. Here, we demonstrate that drought causes enrichment of a distinct set of microbes in roots, composed almost entirely of monoderms, which lack outer membranes and have thick cell walls. We demonstrate that under drought, roots increase the production of many metabolites, and that monoderms inhabiting the drought-treated rhizosphere exhibit increased activity of transporters connected with some of these same compounds. The discovery of this drought-induced enrichment and associated shifts in metabolite exchange between plant and microbe reveal a potential blueprint for manipulating plant microbiomes for improved crop fitness.

Drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome and causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes.

Phylogenetic MLSA and phenotypic analysis identification of three probable novel Pseudomonas species isolated on King George Island, South Shetland, Antarctica

Antarctica harbors a great diversity of microorganisms, including bacteria, archaea, microalgae and yeasts. The Pseudomonas genus is one of the most diverse and successful bacterial groups described to date, but only eight species isolated from Antarctica have been characterized. Here, we present three potentially novel species isolated on King George Island. The most abundant isolates from four different environments, were genotypically and phenotypically characterized. Multilocus sequence analysis and 16S rRNA gene analysis of a sequence concatenate for six genes (16S, aroE, glnS, gyrB, ileS and rpoD), determined one of the isolates to be a new Pseudomonas mandelii strain, while the other three are good candidates for new Pseudomonas species. Additionally, genotype analyses showed the three candidates to be part of a new subgroup within the Pseudomonas fluorescens complex, together with the Antarctic species Pseudomonas antarctica and Pseudomonas extremaustralis. We propose terming this new subgroup P. antarctica. Likewise, phenotypic analyses using API 20 NE and BIOLOG^® corroborated the genotyping results, confirming that all presented isolates form part of the P. fluorescens complex. Pseudomonas genus research on the Antarctic continent is in its infancy. To understand these microorganisms’ role in this extreme environment, the characterization and description of new species is vital.

Elevated nitrogen allows the weak invasive plant Galinsoga quadriradiata to become more vigorous with respect to inter-specific competition

Elevated nitrogen associated with global change is believed to promote the invasion of many vigorous exotic plants. However, it is unclear how a weak exotic plant will respond to elevated nitrogen in the future. In this study, the competitive outcome of a weak invasive plant (Galinsoga quadriradiata) and two non-invasive plants was detected. The plants were subjected to 3 types of culture (mixed, monoculture or one-plant), 2 levels of nitrogen (ambient or elevated at a rate of 2 g m^-2 yr^-1) and 2 levels of light (65% shade or full sunlight). The results showed that elevated nitrogen significantly promoted the growth of both the weak invader and the non-invasive plants in one-plant pots; however, growth promotion was not observed for the non-invasive species in the mixed culture pots. The presence of G. quadriradiata significantly inhibited the growth of the non-invasive plants, and a decreased negative species interaction was detected as a result of elevated nitrogen. Our results suggest that competitive interactions between G. quadriradiata and the non-invasive plants were altered by elevated nitrogen. It provides exceptional evidence that an initially weak invasive plant can become an aggressive invader through elevated nitrogen deposition.

Faster turnover of new soil carbon inputs under increased atmospheric CO2

Rising levels of atmospheric CO₂ frequently stimulate plant inputs to soil, but the consequences of these changes for soil carbon (C) dynamics are poorly understood. Plant-derived inputs can accumulate in the soil and become part of the soil C pool ("new soil C"), or accelerate losses of pre-existing ("old") soil C. The dynamics of the new and old pools will likely differ and alter the long-term fate of soil C, but these separate pools, which can be distinguished through isotopic labeling, have not been considered in past syntheses. Using meta-analysis, we found that while elevated CO₂ (ranging from 550 to 800 parts per million by volume) stimulates the accumulation of new soil C in the short term (<1 year), these effects do not persist in the longer term (1-4 years). Elevated CO₂ does not affect the decomposition or the size of the old soil C pool over either temporal scale. Our results are inconsistent with predictions of conventional soil C models and suggest that elevated CO₂ might increase turnover rates of new soil C. Because increased turnover rates of new soil C limit the potential for additional soil C sequestration, the capacity of land ecosystems to slow the rise in atmospheric CO₂ concentrations may be smaller than previously assumed.