Abstract This chapter aims to provide a mechanistic understanding of the role microbes play in so... more Abstract This chapter aims to provide a mechanistic understanding of the role microbes play in soil carbon (C) storage and propose pathways to include this data to modify existing ecological models. We found that the structure and function of soil microbial communities are controlled by complex interactions of biotic and abiotic site factors, while structural variations in soil microbial communities modulate transformation and/or turnover of soil C. We also demonstrated that inclusion of different microbial groups provides better predictions for different enzymatic activities involved in C degradation. Soil bacteria differ in their survival strategies and ability to influence the terrestrial C pool. We found that the effects of soil management practices of soil C turnover are modulated by the soil aggregate sizes and their associated microbial communities. The control of soil microbial communities on soil C turnover is much more pronounced in smaller sized aggregates. Altogether we demonstrate that soil microbial communities modulate soil C turnover from regional to global scale. Based on our findings, we propose that incorporation of microbial taxonomical and functional information in Earth ecosystem models will reduce uncertainty in model structure as these will represent temporal stability and adaptive responses of microbial communities and their interactions with the environment, which are critical considerations as we face environmental variations and rates of change.
First International Meeting on Microbial Phosphate Solubilization
Three bacterial species, viz. Bacillus megaterium, B. subtilis and Pseudomonas corrugata, origina... more Three bacterial species, viz. Bacillus megaterium, B. subtilis and Pseudomonas corrugata, originally isolated from temperate locations in the Indian Himalayan region, were examined for their growth promotion ability using both pot and field based assays. A local landrace of rice was used as test crop. The three bacterial species exhibited in vitro phosphate solubilizing activity in following order: P. corrugata > B. megaterium > B. subtilis. The bacterial treatments (broth based in pot and charcoal based in field experiments) resulted in improved plant performance. Out of the three treatments, B. subtilis gave best performance resulting in 1.66 and 1.55 fold increase in grain yield of rice in pot and field trials, respectively. Inoculations also stimulated the rhizosphere associated bacterial and actinomycetes populations and suppressed the fungal flora. Colonization of roots by mycorrhizal fungi improved in all the treatments. Out of the three bacterial inoculants, B. subtilis was the best in affecting these changes. Bacterial treatments also resulted in higher values for phosphorus in shoots and grains in inoculated rice plants. The study indicates that the stimulation of native bacterial flora, including mycorrhizae, in and around roots is one of the important parameters playing indirect role in improving the overall plant growth. The study suggests that charcoal based B. subtilis cultures can be developed as an efficient bioinoculant for rice fields in the mountains.
The Australian sugarcane industry is facing a new threat of the currently undiagnosed Yellow Cano... more The Australian sugarcane industry is facing a new threat of the currently undiagnosed Yellow Canopy Syndrome (YCS). Here, we investigated if YCS is linked to detrimental shifts in soil microbial function and/or altered physico-chemical soil properties. We examined changes in rhizosphere soil microbial assemblages, functional gene profiles and microbial activity associated with YCS development. Shifts in soil bacterial and fungal community assemblages with YCS appeared variety-specific with limited consistent trends emerging. However, significant, consistent shifts in the rhizosphere soil metagenome with YCS were found, suggesting that YCS incidence might be linked to changes in specific soil microbial functions. Functional gene categories involved in prokaryotic immune response and in metabolism of compounds present in root exudates were consistently detected in higher abundance in the rhizosphere of YCS-affected plants, while gene categories involved in DNA, RNA and protein processing were consistently less abundant. Soil nutrient status (C, N), extracellular enzyme activity and substrate-induced respiration either did not significantly differ between affected and healthy fields of three sugarcane varieties, or showed inconsistent trends with variety. Altogether, our results did not show a direct link between soil microbial richness, overall soil microbial activity, soil nutrient status and YCS incidence. However, rhizosphere microbial communities responded consistently to YCS incidence by enrichment of genes encoding functions involved in defence against pathogens and root exudate metabolism which may have potential implications for the future development of diagnostic tools and an effective management practice to minimise impact of YCS on farm productivity.
How does climate change affect the diversity and function of the microorganisms in the environmen... more How does climate change affect the diversity and function of the microorganisms in the environment you study? What are the consequences of this change? David A. Hutchins. Some drivers of global change that influence microbial assemblages, such as warming, are common to both marine and terrestrial ecosystems. However, some environmental changes in the ocean also include ocean acidification, deoxygenation and altered circulation of seawater, which are processes that are unique to this environment. These multiple stressors pose a daunting obstacle to predicting the net responses of the planktonic microorganisms that control ocean biological productivity and elemental cycling 1,2. Nevertheless, some generalizations are possible. Ocean acidification frequently inhibits nitrification by archaea and bacteria, whereas deoxygenation promotes microbial denitrification. Nitrogenfixing cyanobacteria should also thrive in a changing ocean, as their growth and fixation rates often benefit from increased carbon dioxide levels and rising temperatures. Taken together, Janet K. Jansson. We are studying two climate-sensitive soil ecosystems: Arctic permafrost and grasslands. Permafrost soil is thawing in large regions of the Arctic, and this has major impacts on functions carried out by the soil microbiome 3. In a frozen state, the stored carbon in permafrost is largely preserved owing to low activity of microorganisms. However, when it thaws, the microorganisms become more active and start to decompose the organic carbon, releasing greenhouse gases such as carbon dioxide and methane to the atmosphere as a result 4. Grassland ecosystems are being affected by changes in precipitation patterns, such as increased, intense rainfall events and/or increasing drought. Soil moisture is paramount for determining the connectivity between spatially discrete soil microorganisms, and, therefore, changes in soil moisture will have a large impact on the ability of soil microorganisms to cycle carbon and other nutrients, including plant-derived compounds that are key inputs into grassland ecosystems.
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to p... more Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.
Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet gro... more Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane-associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the...
The technical comment from Sanderman provides a unique opportunity to deepen our understanding of... more The technical comment from Sanderman provides a unique opportunity to deepen our understanding of the mechanisms explaining the role of paleoclimate in the contemporary distribution of global soil C content, as reported in our article. Sanderman argues that the role of paleoclimate in predicting soil C content might be accounted for by using slowly changing soil properties as predictors. This is a key point that we highlighted in the supplementary materials of our article, which demonstrated, to the degree possible given available data, that soil properties alone cannot account for the unique portion of the variation in soil C explained by paleoclimate. Sanderman also raised an interesting question about how paleoclimate might explain the contemporary amount of C in our soils if such a C is relatively new, particularly in the topsoil layer. There is one relatively simple, yet plausible, reason. A soil with a higher amount of C, a consequence of accumulation over millennia, might pro...
Our findings indicate the importance of paleoclimatic information to improve quantitative predict... more Our findings indicate the importance of paleoclimatic information to improve quantitative predictions of global soil C stocks.
Global demands for food and fibre will increase up to 70% by 2050. This increase in agricultural ... more Global demands for food and fibre will increase up to 70% by 2050. This increase in agricultural productivity needs to be obtained from existing arable land, under harsher climate conditions and with declining soil and water quality. In addition, we have to safeguard our agricultural produce from new, emerging and endemic pests and pathogens. Harnessing natural resources including the 'phytomicrobiome' is proposed to be the most effective approach to improve farm productivity and food quality in a sustainable way, which can also promote positive environmental and social outcomes. Conventional farming that uses chemicals in the form of fertilizers and pesticides has substantially increased agriculture productivity and contributed immensely to food access and poverty alleviation goals. However, excessive and indiscriminate use of these chemicals has resulted in food contamination, negative environmental outcomes and disease resistance which together have a significant impact on human health and food security. The microbiome technology has the potential to minimize this environmental footprint and at the same time sustainably increase the quality and quantity of farm produce with less resource-based inputs. Plants and associated microbiota evolved together and have developed a mutualistic relationship where both partners benefit from the association. However, plant breeding programmes have unintentionally broken
Increasing N inputs and changing rainfall regimes will lead to drastic changes in multiple ecosys... more Increasing N inputs and changing rainfall regimes will lead to drastic changes in multiple ecosystem functions such as nutrient cycling, organic matter decomposition and gas exchange in dryland ecosystems. As fundamental components of drylands, biological soil crusts (biocrusts) play important roles in the regulation of responses of multiple ecosystem functions to global environmental changes. Biocrusts are home to highly functional microbial communities; however little is known on the role of microbial communities associated with different biocrust species in regulating the response of multiple ecosystem functions to global change. Here, we conducted a microcosm experiment to evaluate the roles of biocrust-forming lichens (Diploschistes thunbergianus, Psora crystallifera and Xanthoparmelia reptans) in mediating the effects of simulated changes in rainfall frequency and nitrogen (N) addition on soil multifunctionality involving nutrient availability, greenhouse gas flux and enzyme activities. The three biocrust species supported different levels of soil bacterial diversity, and specific community composition as revealed by MiSeq sequencing. Biocrust species always promoted multiple functions related to carbon, nitrogen and phosphorus cycling compared to bare ground, with X. reptans having the highest effect on multifunctionality. Most importantly, the relative abundance of specific microbial communities associated with different lichen species modulates the response of multifunctionality to impacts of water frequency (negative) and N addition (positive). Our results suggest that biocrust species could regulate global change impacts on soil multifunctionality in drylands, although the strength and direction vary among the biocrust species. These findings highlight the importance of preserving biocrusts as hotspots of microbial genetic resources and ecosystem functioning in drylands.
Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in ... more Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real-world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant-microbe interactions to breed 'microbe-optimized plants'. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security. Sustainable development goals and agriculture productivity
Abstract This chapter aims to provide a mechanistic understanding of the role microbes play in so... more Abstract This chapter aims to provide a mechanistic understanding of the role microbes play in soil carbon (C) storage and propose pathways to include this data to modify existing ecological models. We found that the structure and function of soil microbial communities are controlled by complex interactions of biotic and abiotic site factors, while structural variations in soil microbial communities modulate transformation and/or turnover of soil C. We also demonstrated that inclusion of different microbial groups provides better predictions for different enzymatic activities involved in C degradation. Soil bacteria differ in their survival strategies and ability to influence the terrestrial C pool. We found that the effects of soil management practices of soil C turnover are modulated by the soil aggregate sizes and their associated microbial communities. The control of soil microbial communities on soil C turnover is much more pronounced in smaller sized aggregates. Altogether we demonstrate that soil microbial communities modulate soil C turnover from regional to global scale. Based on our findings, we propose that incorporation of microbial taxonomical and functional information in Earth ecosystem models will reduce uncertainty in model structure as these will represent temporal stability and adaptive responses of microbial communities and their interactions with the environment, which are critical considerations as we face environmental variations and rates of change.
First International Meeting on Microbial Phosphate Solubilization
Three bacterial species, viz. Bacillus megaterium, B. subtilis and Pseudomonas corrugata, origina... more Three bacterial species, viz. Bacillus megaterium, B. subtilis and Pseudomonas corrugata, originally isolated from temperate locations in the Indian Himalayan region, were examined for their growth promotion ability using both pot and field based assays. A local landrace of rice was used as test crop. The three bacterial species exhibited in vitro phosphate solubilizing activity in following order: P. corrugata > B. megaterium > B. subtilis. The bacterial treatments (broth based in pot and charcoal based in field experiments) resulted in improved plant performance. Out of the three treatments, B. subtilis gave best performance resulting in 1.66 and 1.55 fold increase in grain yield of rice in pot and field trials, respectively. Inoculations also stimulated the rhizosphere associated bacterial and actinomycetes populations and suppressed the fungal flora. Colonization of roots by mycorrhizal fungi improved in all the treatments. Out of the three bacterial inoculants, B. subtilis was the best in affecting these changes. Bacterial treatments also resulted in higher values for phosphorus in shoots and grains in inoculated rice plants. The study indicates that the stimulation of native bacterial flora, including mycorrhizae, in and around roots is one of the important parameters playing indirect role in improving the overall plant growth. The study suggests that charcoal based B. subtilis cultures can be developed as an efficient bioinoculant for rice fields in the mountains.
The Australian sugarcane industry is facing a new threat of the currently undiagnosed Yellow Cano... more The Australian sugarcane industry is facing a new threat of the currently undiagnosed Yellow Canopy Syndrome (YCS). Here, we investigated if YCS is linked to detrimental shifts in soil microbial function and/or altered physico-chemical soil properties. We examined changes in rhizosphere soil microbial assemblages, functional gene profiles and microbial activity associated with YCS development. Shifts in soil bacterial and fungal community assemblages with YCS appeared variety-specific with limited consistent trends emerging. However, significant, consistent shifts in the rhizosphere soil metagenome with YCS were found, suggesting that YCS incidence might be linked to changes in specific soil microbial functions. Functional gene categories involved in prokaryotic immune response and in metabolism of compounds present in root exudates were consistently detected in higher abundance in the rhizosphere of YCS-affected plants, while gene categories involved in DNA, RNA and protein processing were consistently less abundant. Soil nutrient status (C, N), extracellular enzyme activity and substrate-induced respiration either did not significantly differ between affected and healthy fields of three sugarcane varieties, or showed inconsistent trends with variety. Altogether, our results did not show a direct link between soil microbial richness, overall soil microbial activity, soil nutrient status and YCS incidence. However, rhizosphere microbial communities responded consistently to YCS incidence by enrichment of genes encoding functions involved in defence against pathogens and root exudate metabolism which may have potential implications for the future development of diagnostic tools and an effective management practice to minimise impact of YCS on farm productivity.
How does climate change affect the diversity and function of the microorganisms in the environmen... more How does climate change affect the diversity and function of the microorganisms in the environment you study? What are the consequences of this change? David A. Hutchins. Some drivers of global change that influence microbial assemblages, such as warming, are common to both marine and terrestrial ecosystems. However, some environmental changes in the ocean also include ocean acidification, deoxygenation and altered circulation of seawater, which are processes that are unique to this environment. These multiple stressors pose a daunting obstacle to predicting the net responses of the planktonic microorganisms that control ocean biological productivity and elemental cycling 1,2. Nevertheless, some generalizations are possible. Ocean acidification frequently inhibits nitrification by archaea and bacteria, whereas deoxygenation promotes microbial denitrification. Nitrogenfixing cyanobacteria should also thrive in a changing ocean, as their growth and fixation rates often benefit from increased carbon dioxide levels and rising temperatures. Taken together, Janet K. Jansson. We are studying two climate-sensitive soil ecosystems: Arctic permafrost and grasslands. Permafrost soil is thawing in large regions of the Arctic, and this has major impacts on functions carried out by the soil microbiome 3. In a frozen state, the stored carbon in permafrost is largely preserved owing to low activity of microorganisms. However, when it thaws, the microorganisms become more active and start to decompose the organic carbon, releasing greenhouse gases such as carbon dioxide and methane to the atmosphere as a result 4. Grassland ecosystems are being affected by changes in precipitation patterns, such as increased, intense rainfall events and/or increasing drought. Soil moisture is paramount for determining the connectivity between spatially discrete soil microorganisms, and, therefore, changes in soil moisture will have a large impact on the ability of soil microorganisms to cycle carbon and other nutrients, including plant-derived compounds that are key inputs into grassland ecosystems.
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to p... more Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.
Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet gro... more Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane-associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the...
The technical comment from Sanderman provides a unique opportunity to deepen our understanding of... more The technical comment from Sanderman provides a unique opportunity to deepen our understanding of the mechanisms explaining the role of paleoclimate in the contemporary distribution of global soil C content, as reported in our article. Sanderman argues that the role of paleoclimate in predicting soil C content might be accounted for by using slowly changing soil properties as predictors. This is a key point that we highlighted in the supplementary materials of our article, which demonstrated, to the degree possible given available data, that soil properties alone cannot account for the unique portion of the variation in soil C explained by paleoclimate. Sanderman also raised an interesting question about how paleoclimate might explain the contemporary amount of C in our soils if such a C is relatively new, particularly in the topsoil layer. There is one relatively simple, yet plausible, reason. A soil with a higher amount of C, a consequence of accumulation over millennia, might pro...
Our findings indicate the importance of paleoclimatic information to improve quantitative predict... more Our findings indicate the importance of paleoclimatic information to improve quantitative predictions of global soil C stocks.
Global demands for food and fibre will increase up to 70% by 2050. This increase in agricultural ... more Global demands for food and fibre will increase up to 70% by 2050. This increase in agricultural productivity needs to be obtained from existing arable land, under harsher climate conditions and with declining soil and water quality. In addition, we have to safeguard our agricultural produce from new, emerging and endemic pests and pathogens. Harnessing natural resources including the 'phytomicrobiome' is proposed to be the most effective approach to improve farm productivity and food quality in a sustainable way, which can also promote positive environmental and social outcomes. Conventional farming that uses chemicals in the form of fertilizers and pesticides has substantially increased agriculture productivity and contributed immensely to food access and poverty alleviation goals. However, excessive and indiscriminate use of these chemicals has resulted in food contamination, negative environmental outcomes and disease resistance which together have a significant impact on human health and food security. The microbiome technology has the potential to minimize this environmental footprint and at the same time sustainably increase the quality and quantity of farm produce with less resource-based inputs. Plants and associated microbiota evolved together and have developed a mutualistic relationship where both partners benefit from the association. However, plant breeding programmes have unintentionally broken
Increasing N inputs and changing rainfall regimes will lead to drastic changes in multiple ecosys... more Increasing N inputs and changing rainfall regimes will lead to drastic changes in multiple ecosystem functions such as nutrient cycling, organic matter decomposition and gas exchange in dryland ecosystems. As fundamental components of drylands, biological soil crusts (biocrusts) play important roles in the regulation of responses of multiple ecosystem functions to global environmental changes. Biocrusts are home to highly functional microbial communities; however little is known on the role of microbial communities associated with different biocrust species in regulating the response of multiple ecosystem functions to global change. Here, we conducted a microcosm experiment to evaluate the roles of biocrust-forming lichens (Diploschistes thunbergianus, Psora crystallifera and Xanthoparmelia reptans) in mediating the effects of simulated changes in rainfall frequency and nitrogen (N) addition on soil multifunctionality involving nutrient availability, greenhouse gas flux and enzyme activities. The three biocrust species supported different levels of soil bacterial diversity, and specific community composition as revealed by MiSeq sequencing. Biocrust species always promoted multiple functions related to carbon, nitrogen and phosphorus cycling compared to bare ground, with X. reptans having the highest effect on multifunctionality. Most importantly, the relative abundance of specific microbial communities associated with different lichen species modulates the response of multifunctionality to impacts of water frequency (negative) and N addition (positive). Our results suggest that biocrust species could regulate global change impacts on soil multifunctionality in drylands, although the strength and direction vary among the biocrust species. These findings highlight the importance of preserving biocrusts as hotspots of microbial genetic resources and ecosystem functioning in drylands.
Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in ... more Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real-world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant-microbe interactions to breed 'microbe-optimized plants'. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security. Sustainable development goals and agriculture productivity
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Papers by Pankaj Trivedi