Application of ecological theory to explain microbial regulation of soil function

A growing body of experimental and observational studies have indicated that plant and animal diversity drives ecosystem function and stability in terrestrial ecosystems. Therefore, it is of paramount importance to identify the consequences of biodiversity loss to assess long-term sustainability of ecosystem functions and services (e.g. climate regulation and nutrient cycling). Soil microbial communities represent one of the most diverse and complex natural communities and are responsible for many ecologically and economically important processes. For example, soil microbes play critical roles in regulating nutrient cycling, decomposition of organic matter, and gas emission. These ecological processes are fundamental for human wellbeing. Despite their importance and complexity, soil microbes receive little attention in the ongoing debate regarding global biodiversity loss, global change and conservation issues, primarily due to the perceived functional redundancy and the large diversity of the soil microbial community. This is no accident; there is a lack of theoretical and experimental protocols which demonstrate microbial regulation of soil ecosystem processes. Consequently, much less is known of the role of microbial diversity in controlling ecosystem functioning. This is critical knowledge gap which hinders inclusion of microbial community response in simulation models or management and policy decisions. Therefore, this research investigated the relationship between microbial diversity and ecosystem functioning (BEF) and resistance to better understand the consequences of microbial diversity loss on ecosystem function and sustainability. To achieve this, my project was divided into experimental (Chapters 2- 4) and observational (Chapters 3 and 5) studies. Each chapter in this thesis will highlight the importance of microbial diversity in ecosystem function. In summary, my study provided direct evidence of relationship and the shape of relationships between microbial diversity and ecosystem functions and suggested that any loss of microbial diversity will have at least proportional decline in the process rates. Particularly microbial community richness and composition were found to be important, yet independent drivers of multiple ecosystem functions. These results highlight that, belowground microbial diversity is as important as above ground diversity in maintaining ecosystem services. This study is also the first to investigating the drivers of microbial nitrifiers at the global scale. Overall, results from this thesis demonstrate that microbial diversity should be explicitly considered in all biodiversity conservation debates and management decisions and indicated that inclusion of microbial data in predictive models are required to improve predictions to ensure that informed environmental policy decisions are made to sustain ecosystem function under predicted global climate change scenarios

Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.This research is supported by the Australian Research Council projects (DP170104634 and DP190103714), by the European Research Council (BIOCOM project, ERC Grant agreement n°242658) and by the Spanish Ministerio de Economía y Competitividad (BIOMOD project, ref. CGL2013-44661-R). M.D-B. acknowledges support from the Marie Sklodowska-Curie Actions of the Horizon 2020 Framework Programme H2020-MSCA-IF-2016 under REA grant agreement n°702057. FTM acknowledges support from the European Research Council (BIODESERT project, ERC Grant agreement n°647038)

Litter and soil biodiversity jointly drive ecosystem functions

10 páginas.- 4 figuras.- 64 referencias.- Additional supporting information can be found online in the Supporting Information section at the end of this articleThe decomposition of litter and the supply of nutrients into and from the soil are two fundamental processes through which the above- and belowground world interact. Microbial biodiversity, and especially that of decomposers, plays a key role in these processes by helping litter decomposition. Yet the relative contribution of litter diversity and soil biodiversity in supporting multiple ecosystem services remains virtually unknown. Here we conducted a mesocosm experiment where leaf litter and soil biodiversity were manipulated to investigate their influence on plant productivity, litter decomposition, soil respiration, and enzymatic activity in the littersphere. We showed that both leaf litter diversity and soil microbial diversity (richness and community composition) independently contributed to explain multiple ecosystem functions. Fungal saprobes community composition was especially important for supporting ecosystem multifunctionality (EMF), plant production, litter decomposition, and activity of soil phosphatase when compared with bacteria or other fungal functional groups and litter species richness. Moreover, leaf litter diversity and soil microbial diversity exerted previously undescribed and significantly interactive effects on EMF and multiple individual ecosystem functions, such as litter decomposition and plant production. Together, our work provides experimental evidence supporting the independent and interactive roles of litter and belowground soil biodiversity to maintain ecosystem functions and multiple services.SEL acknowledges support from the National Natural Science Foundation of China (grant no. 32101491), fellowship of China Postdoctoral Science Foundation (2022T150375; 2021M701968), and Yunnan Science and Technology Talent and Platform Program (202105AG070002). GYZ acknowledges support from the Humbodlt Research Foundation. JP acknowledges support from the Ramon y Cajal program from the MICINN (RYC-2021-033454). ROH is funded by the Ramon y Cajal program of the MICINN (RYC-2017 22032), by the R & amp;D Project of the Ministry of Science and Innovation PID2019-106004RA-I00 funded by MCIN/AEI/10.13039/501100011033, and by the European Agricultural Fund for Rural Development (EAFRD) through the "Aid to operational groups of the European Association of Innovation (AEI) in terms of agricultural productivity and sustainability", Reference: GOPC-CA-20-0001. BKS acknowledge funding from Australian Research Council (DP210102081). MDB acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 and TED2021-130908B-C41 funded by MCIN/AEI/10.13039/501100011033. Open Access funding enabled and organized by Projekt DEAL.Peer reviewe

High spin band structures in doubly-odd 194^{194}Tl

The high-spin states in odd-odd $^{194}$Tl nucleus have been studied by populating them using the $^{185,187}$Re($^{13}$C, xn) reactions at 75 MeV of beam energy. $\gamma-\gamma$ coincidence measurement has been performed using the INGA array with a digital data acquisition system to record the time stamped data. Definite spin-parity assignment of the levels was made from the DCO ratio and the IPDCO ratio measurements. The level scheme of $^{194}$Tl has been extended up to 4.1 MeV in excitation energy including 19 new gamma ray transitions. The $\pi h_{9/2} \otimes \nu i_{13/2}$ band, in the neighboring odd-odd Tl isotopes show very similar properties in both experimental observables and calculated shapes. Two new band structures, with 6-quasiparticle configuration, have been observed for the first time in $^{194}$Tl. One of these bands has the characteristics of a magnetic rotational band. The cranked shell model calculations, using a deformed Woods-Saxon potential, have been performed to obtain the total Routhian surfaces in order to study the shapes of the bands and the band crossing in $^{194}$Tl. The semiclassical formalism has been used to describe the magnetic rotational band.Comment: Accepted for publication in Physical Review

Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships.

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models

Harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus (Ca.) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant–microbe and plant–insect interactions of these pathogens have demonstrated that plant–microbe–insect interactions have far reaching consequences for the functioning and evolution of the organisms involved. These interactions take place within complex pathosystems and are shaped by a myriad of biotic and abiotic factors. However, our current understanding of these processes and their implications for the establishment and spread of insect-borne diseases remains limited. This article highlights the molecular, ecological, and evolutionary aspects of interactions among insects, plants, and their associated microbial communities with a focus on insect vectored and phloemlimited pathogens belonging to Ca. Phytoplasma and Ca. Liberibacter species. We propose that innovative and interdisciplinary research aimed at linking scales from the cellular to the community level will be vital for increasing our understanding of the mechanisms underpinning plant–insect–microbe interactions. Examination of such interactions could lead us to applied solutions for sustainable disease and pest management

Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships.

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems

Uncovering potential soil drivers of soils pathogen suppression represent an essential step in order to develop alternative and sustainable management strategies for disease control and increased soil health. In this study, we tested the potential role of keystone microbial taxa and chemical/physical properties in the suppression (referred to as soil suppressiveness) of the soil-borne model pathogen Fusarium oxysporum using soil samples from various crop producing agro-ecosystems in Australia. Using random forest, we identified bacteria belonging to the phyla Actinobacteria, Firmicutes and Acidobacteria as the major microbial predictors for soil suppressiveness at a continental scale. Structural equation modeling approach revealed strong relationship between the relative abundance of phylum Actinobacteria and soil functions carried out by soil microbial communities (soil functioning) with pathogen inhibition. Overall our study provided a mechanistic framework showing how microbial communities, soil functionality, and abiotic properties being antagonistic to soil pathogens are linked and interactively shape the suppressive potential of soils at continental scale. This information, upon further validation can be incorporated in risk management tools for developing novel concepts such as “Know before you Sow” leading to increased farm productivity and profitability

Microbial richness and composition independently drive soil multifunctionality

Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend. We used two independent approaches (i.e. experimental and observational), and applied statistical modelling to identify the role and relative importance of bacterial richness and composition in driving multifunctionality (here defined as seven measures of respiration and enzyme activities). In the observational study, we measured soil microbial communities and functions in both tree- and bare soil-dominated microsites at 22 locations across a 1,200 km transect in southeastern Australia. In the experimental study we used soils from two of those locations and developed gradients of bacterial diversity and composition through inoculation of sterilized soils. Microbial richness and the relative abundance of Gammaproteobacteria, Actinobacteria, and Bacteroidetes were positively related to multifunctionality in both the observational and experimental approaches; however, only Bacteroidetes was consistently selected as a key predictor of multifunctionality across all experimental approaches and statistical models used here. Moreover, our results, from two different approaches, provide evidence that microbial richness and composition are both important, yet independent, drivers of multiple ecosystem functions. Overall, our findings advance our understanding of the mechanisms underpinning relationships between microbial diversity and ecosystem functionality in terrestrial ecosystems, and further suggest that information on microbial richness and composition needs to be considered when formulating sustainable management and conservation policies, and when predicting the effects of global change on ecosystem functions. A plain language summary is available for this article