Land-use drives the temporal stability and magnitude of soil microbial functions and modulates climate effects

Soil microbial community functions are essential indicators of ecosystem multifunctionality in managed land-use systems. Going forward, the development of adaptation strategies and predictive models under future climate scenarios will require a better understanding of how both land-use and climate disturbances influence soil microbial functions over time. Between March and November 2018, we assessed the effects of climate change on the magnitude and temporal stability of soil basal respiration, soil microbial biomass and soil functional diversity across a range of land-use types and intensities in a large-scale field experiment. Soils were sampled from five common land-use types including conventional and organic croplands, intensive and extensive meadows, and extensive pastures, under ambient and projected future climate conditions (reduced summer precipitation and increased temperature) at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Land-use and climate treatment interaction effects were significant in September, a month when precipitation levels slightly rebounded following a period of drought in central Germany: compared to ambient climate, in future climate treatments, basal respiration declined in pastures and increased in intensive meadows, functional diversity declined in pastures and croplands, and respiration-to-biomass ratio increased in intensive and extensive meadows. Low rainfall between May and August likely strengthened soil microbial responses toward the future climate treatment in September. Although microbial biomass showed declining levels in extensive meadows and pastures under future climate treatments, overall, microbial function magnitudes were higher in these land-use types compared to croplands, indicating that improved management practices could sustain high microbial ecosystem functioning in future climates. In contrast to our hypothesis that more disturbed land-use systems would have destabilized microbial functions, intensive meadows and organic croplands showed stabilized soil microbial biomass compared to all other land-use types, suggesting that temporal stability, in addition to magnitude-based measurements, may be useful for revealing context-dependent effects on soil ecosystem functioning

The influence of elevated CO2 and soil depth on rhizosphere activity and nutrient availability in a mature Eucalyptus woodland

Elevated carbon dioxide (eCO2) in the atmosphere increases forest biomass productivity but only where soil nutrients, particularly nitrogen (N) and phosphorus (P), are not limiting growth. eCO2, in turn, can impact rhizosphere nutrient availability. Our current understanding of nutrient cy cling under eCO2 is mainly derived from surface soil, leaving mechanisms of the impact of eCO2 on rhizosphere nutrient availability at deeper depths unexplored. To investigate the influence of eCO2 on nutrient availability in soil at depth, we studied various C, N, and P pools (extractable, microbial biomass, total soil C and N, and mineral-associated P) and nutrient cycling processes (enzyme activity and gross N mineralisation) associated with C, N, and P cycling in both bulk and rhizosphere soil at different depths at the Free Air CO2 enrichment facility in a native Australian mature Eucalyptus woodland (EucFACE) on a nutrient-poor soil. We found de creasing nutrient availability and gross N mineralisation with depth; however, this depth-associated decrease was reduced under eCO2, which we suggest is due to enhanced root influence. Increases in available PO3− 4 , adsorbed P, and the C : N and C : P ratio of enzyme activity with depth were observed. We conclude that the influences of roots and of eCO2 can affect available nutrient pools and processes well beyond the surface soil of a mature forest ecosystem. Our findings indicate a faster recycling of nutrients in the rhizosphere, rather than additional nutrients becoming available through soil organic matter (SOM) decomposition. If the plant growth response to eCO2 is reduced by the constraints of nutrient limitations, then the current results would call to question the potential for mature tree ecosystems to fix more C as biomass in response to eCO2. Future studies should address how accessible the available nutrients at depth are to deeply rooted plants and if fast recycling of nutrients is a meaningful contribution to biomass production and the accumulation of soil C in response to eCO2

Synthetic community improves crop performance and alters rhizosphere microbial communities

Introduction: Harnessing synthetic communities (SynCom) of plant growth‐promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowledge gaps that constrain field efficacy of SynCom and hence large‐ scale adoption by the farming community. Material & Methods: In this study, a SynCom of four PGP microbial species was constructed and applied to either as seed dressing (treatment T1, applied at the time of sowing) or to soil (treatment T2, applied in soil at true leaf stage) across five different cotton (Gossypium hirsutum) cultivars. The impact of SynCom on plant growth, rhizosphere microbiome and soil nutrient availability, and how this was modified by plant variety and mode of applications, was assessed. Results: Results showed that the seed application of SynCom had the strongest positive impact on overall plant fitness, resulting in higher germination (14.3%), increased plant height (7.4%) and shoot biomass (5.4%). A significant increase in the number of flowers (10.4%) and yield (8.5%) was also observed in T1. The soil nitrate availability was enhanced by 28% and 55% under T1 and T2, respectively. Results further suggested that SynCom applications triggered enrichment of members from bacterial phyla Actinobacteria, Firmicutes and Cyanobacteria in the rhizosphere. A shift in fungal communities was also observed, with a significant increase in the relative abundance of fungi from phyla Chytridiomycota and Basidiomycota in SynCom treatments. A structural equation model suggested that SynCom directly increased crop productivity but also indirectly via impacting the alpha diversity of bacteria. Conclusion: Overall, this study provides mechanistic evidence that SynCom applications can shift rhizosphere microbial communities and improve soil fertility, plant growth, and crop productivity, suggesting that their use could contribute toward sustainable increase in farm productivity

Harnessing plant-microbe interactions for enhancing farm productivity

Declining soil fertility and farm productivity is a major global concern in order to achieve food security for a burgeoning world population. It is reported that improving soil health alone can increase productivity by 10–15% and in combination with efficient plant traits, farm productivity can be increased up to 50–60%. In this article we explore the emerging microbial and bioengineering technologies, which can be employed to achieve the transformational increase in farm productivity and can simultaneously enhance environmental outcomes i.e., low green house gas (GHG) emissions. We argue that metagenomics, meta-transcriptomics and metabolomics have potential to provide fundamental knowledge on plant-microbes interactions necessary for new innovations to increase farm productivity. Further, these approaches provide tools to identify and select novel microbial/gene resources which can be harnessed in transgenic and designer plant technologies for enhanced resource use efficiencies

Ecosystem function and services : regulating services : atmospheric composition and climate regulation

Climate change is most likely the greatest challenge that humans will face this century. The role of microbiota in determining the Earth's atmospheric composition, and hence climate, started with the origin of life. From the first molecules of oxygen produced by marine cyanobacteria 3.5 thousand million years ago, to the production of methane by archaea (see page 32) in the warm, carbon-rich swamps of the Carboniferous period, microbial processes have long been key drivers of, and responders to, climate change. Throughout the history of our living planet, microbes have been the main modulators in determining atmospheric concentrations of greenhouse gases (GHG), including carbon dioxide (CO2), methane (CH) and nitrous oxide (N20). [129

Drug discovery from uncultivable microorganisms

Environmental microbes are a major source of drug discovery, and several microbial products (antibiotics, anti-tumour products, immunosuppressants and others) are used routinely for human therapies. Most of these products were obtained from cultivable (<1%) environmental microbes, and this means that the vast majority of microbes were not targeted for drug discovery. With the advent of new and emerging technologies, we are poised to harvest novel drugs from the so-called 'uncultivable' microbes. In this article, we propose how a multidisciplinary approach combining different technologies can expedite and revolutionize drug discovery from uncultivable microbes and examine the current limitations of technologies and strategies to overcome such limitations that might further expand the promise of drugs from environmental microbes

Elevated carbon dioxide increases soil nitrogen and phosphorus availability in a phosphorus-limited Eucalyptus woodland

Free-Air CO2 Enrichment (FACE) experiments have demonstrated increased plant productivity in response to elevated (e)CO2, with the magnitude of responses related to soil nutrient status. Whilst understanding nutrient constraints on productivity responses to eCO2 is crucial to predicting carbon uptake and storage, very little is known about how eCO2 affects nutrient cycling in phosphorus (P)-limited ecosystems. Our study investigates eCO2 effects on soil N and P dynamics at the EucFACE experiment in Western Sydney over an 18 month period. Three ambient and three eCO2 (+150 ppm) FACE rings were installed in a P-limited, mature Cumberland Plain Eucalyptus woodland. Levels of plant accessible nutrients, evaluated using ion exchange resins, were increased under eCO2, compared to ambient, for nitrate (+93%), ammonium (+12%) and phosphate (+54%). There was a strong seasonality to responses, particularly for phosphate, resulting in a relatively greater stimulation in available P, compared to N, under eCO2 in spring and summer. eCO2 was also associated with faster nutrient turnover rates in the first six months of the experiment, with higher N (+175%) and P (+211%) mineralisation rates compared to ambient rings, although this difference did not persist. Seasonally-dependant effects of eCO2 were seen for concentrations of dissolved organic carbon in soil solution (+31%), and there was also a reduction in bulk-soil pH (-0.18 units) observed under eCO2. These results demonstrate that CO2 fertilisation increases nutrient availability - particularly for phosphate - in P-limited soils, likely via increased plant belowground investment in labile carbon and associated enhancement of microbial turnover of organic matter and mobilisation of chemically-bound P. Early evidence suggests that there is the potential for the observed increases in P availability to support increased ecosystem C-accumulation under future predicted CO2 concentrations

Discrimination of soils at regional and local levels using bacterial and fungal T-RFLP profiling

DNA profiling of microbial communities has been proposed as a tool for forensic comparison of soils, but its potential to discriminate between soils from similar land use and ⁄ or geographic location has been largely unexplored. We tested the ability of terminal restriction fragment length polymorphism (T-RFLP) to discriminate between soils from 10 sites within the Greater Wellington region, New Zealand, based on their bacterial and fungal DNA profiles. Significant differences in bacterial and fungal communities between soils collected from all but one pair of sites were demonstrated. In some instances, specific terminal restriction fragments were associated with particular sites. Patch discrimination was evident within several sites, which could prove useful for site-specific matching (e.g., matching shoe ⁄ car tire print to an object). These results support the need for further understanding of the spatial distribution of soil microbial communities before DNA profiling of soil microbial communities can be applied to the forensic context

New and Future Developments in Microbial Biotechnology and Bioengineering: Phytomicrobiome for Sustainable Agriculture

New and Future Developments in Microbial Biotechnology and Bioengineering: Phytomicrobiome for Sustainable Agriculture provides a comprehensive overview of the phytomicrobiome and a holistic approach for its various mechanisms, including plant growth, nutrient content, crop yield improvement, soil fertility, and health management. This book explores the genus- and species-specific endophytic microbes for developing an efficient indigenous microbial consortium for enhancing the productivity of sustainable agriculture. An essential resource for students, researchers, and scientists in the fields of biotechnology, microbiology, agronomy, and the plant protection sciences, New and Future Developments in Microbial Biotechnology and Bioengineering: Phytomicrobiome for Sustainable Agriculture highlights the plant growth-promoting activities of the phytomicrobiome and focuses on both its basic and applied aspects and the significant role they play in plant protection

Impact of biotic and abiotic interaction on soil microbial communities and functions : a field study

Interactions between plants, soils and microbes regulate terrestrial ecosystem functioning. Biotic and abiotic interactions can strongly affect the community structure which in turn will impact on ecological processes. Plant species with different ecophysiological traits can exert strong effects on soil biological properties. Our objective was to investigate and identify the effects of different biotic and abiotic variables on soil microbial community structure and functions and to examine if plant species with different physiological traits support different microbial communities in soils. Here, we show that 3 years of the presence of plants had direct impacts on soil function in terms of total heterotrophic respiration and on microbial biomass and microbial community structure. However, the plant species specific impact on bacterial community structure was weak, and differences were mainly driven by sample field location. The fungal community analysis gave similar results, with soil location being the most important factor driving fungal community structure. The effect of plant species on fungal community structure was weak but statistically significant. There was a strong concordance between bacterial and fungal communities (P < 0.001) which suggested that the bacteria and fungi have an influence on shaping the structure of each other’s community. Among the abiotic factors, moisture had a comparatively higher impact on bacterial communities compared to soil N and C. However, the fungal community was not affected by the soil moisture but soil N and C had a stronger impact than on the bacterial community. These results indicate that the microbial community structure in the natural environment is influenced by interactions between both biotic and abiotic factors