Dr Jen Wood | Microbial ecologist | La Trobe University http://environmentalmicro.weebly/Jen.html
Small things matter: unearthing soil microbe interactions that govern plant and ecosystem health
What do food security, cleaning-up pollution and saving the rainforest have in common? Plants and microbes working together! Microorganisms that live in the soil, known as the soil microbiome, are the microscopic foundation of all terrestrial ecosystems and the space where the soil microbiome meets plant roots is called the rhizosphere. Within the rhizosphere, important interactions take place that can govern plant and even ecosystem health.
In the last decade, technological advances have helped scientists begin to catalogue the millions of microbes living under our feet. Yet, just as a list of plant species cannot explain how an ecosystem functions, neither can these lists of microbial species complete our understanding of what soil and rhizosphere microbial communities are doing.
My research uses a trait-based (rather than species based) approach which allows us to look beyond the names and begin understanding how soil microbes are interacting with each other and with the plants that they encounter – how do they compete or cooperate with one another and which of these interactions are most common? If the balance of interactions within a soil community change, what is the impact on plant growth or productivity? Is there a relationship between the types of microbial interactions we see in soils and the kinds of plant communities they can support?
Understanding of soil microbial communities and how they interact with plants is one of the final frontiers for improving agricultural productivity , technologies that use plants to clean-up contaminated soils and even for understanding how rare or endangered plant communities, such as diversity-rich rainforests, are formed and maintained. In the long-term, this research strives to generate applied outcomes such as the development of new strategies for increased agricultural sustainability or improved conservation management practices.
Abstract: Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.
Pub.: 28 Nov '14, Pinned: 27 Oct '17
Abstract: Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species-rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short-term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community-weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon-to-nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long-term climate change effects, especially in nutrient-poor systems with slow-growing vegetation.
Pub.: 09 Jan '17, Pinned: 27 Oct '17
Abstract: Soil microorganisms are clearly a key component of both natural and managed ecosystems. Despite the challenges of surviving in soil, a gram of soil can contain thousands of individual microbial taxa, including viruses and members of all three domains of life. Recent advances in marker gene, genomic and metagenomic analyses have greatly expanded our ability to characterize the soil microbiome and identify the factors that shape soil microbial communities across space and time. However, although most soil microorganisms remain undescribed, we can begin to categorize soil microorganisms on the basis of their ecological strategies. This is an approach that should prove fruitful for leveraging genomic information to predict the functional attributes of individual taxa. The field is now poised to identify how we can manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve our understanding of how terrestrial ecosystems will respond to environmental change.
Pub.: 22 Aug '17, Pinned: 26 Oct '17
Abstract: Despite the growing appreciation for the functional diversity of arbuscular mycorrhizal (AM) fungi, our understanding of the causes and consequences of this diversity is still poor. In this opinion article, we review published data on AM fungal functional traits and attempt to identify major axes of life history variation. We propose that a life history classification system based on the grouping of functional traits, such as Grime's C-S-R (competitor, stress tolerator, ruderal) framework, can help to explain life history diversification in AM fungi, successional dynamics, and the spatial structure of AM fungal assemblages. Using a common life history classification framework for both plants and AM fungi could also help in predicting probable species associations in natural communities and increase our fundamental understanding of the interaction between land plants and AM fungi.
Pub.: 13 Jun '13, Pinned: 26 Oct '17
Abstract: While it is well established that plants associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi cycle carbon (C) and nutrients in distinct ways, we have a limited understanding of whether varying abundance of ECM and AM plants in a stand can provide integrative proxies for key biogeochemical processes. We explored linkages between the relative abundance of AM and ECM trees and microbial functioning in three hardwood forests in southern Indiana, USA. Across each site's 'mycorrhizal gradient', we measured fungal biomass, fungal : bacterial (F : B) ratios, extracellular enzyme activities, soil carbon : nitrogen ratio, and soil pH over a growing season. We show that the percentage of AM or ECM trees in a plot promotes microbial communities that both reflect and determine the C to nutrient balance in soil. Soils dominated by ECM trees had higher F : B ratios and more standing fungal biomass than AM stands. Enzyme stoichiometry in ECM soils shifted to higher investment in extracellular enzymes needed for nitrogen and phosphorus acquisition than in C-acquisition enzymes, relative to AM soils. Our results suggest that knowledge of mycorrhizal dominance at the stand or landscape scale may provide a unifying framework for linking plant and microbial community dynamics, and predicting their effects on ecological function.
Pub.: 06 Dec '16, Pinned: 26 Oct '17
Abstract: Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this work, we characterized antagonistic activities and nutrient use among Streptomyces and Fusarium from the rhizosphere of Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants growing in communities of 1 (monoculture) or 16 (polyculture) plant species. Streptomyces from monoculture were more antagonistic against Fusarium than those from polyculture. In contrast, Fusarium isolates from polyculture had greater inhibitory capacities against Streptomyces than isolates from monoculture. Although Fusarium isolates had on average greater niche widths, the collection of Streptomyces isolates in total used a greater diversity of nutrients for growth. Plant richness, but not plant host, influenced the potential for resource competition between the two taxa. Fusarium isolates had greater niche overlap with Streptomyces in monoculture than polyculture, suggesting greater potential for Fusarium to competitively challenge Streptomyces in monoculture plant communities. In contrast, Streptomyces had greater niche overlap with Fusarium in polyculture than monoculture, suggesting that Fusarium experiences greater resource competition with Streptomyces in polyculture than monoculture. These patterns of competitive and inhibitory phenotypes among Streptomyces and Fusarium populations are consistent with selection for Fusarium-antagonistic Streptomyces populations in the presence of strong Fusarium resource competition in plant monocultures. Similarly, these results suggest selection for Streptomyces-inhibitory Fusarium populations in the presence of strong Streptomyces resource competition in more diverse plant communities. Thus, landscape-scale variation in plant species richness may be critical to mediating the coevolutionary dynamics and selective trajectories for inhibitory and nutrient use phenotypes among Streptomyces and Fusarium populations in soil, with significant implications for microbial community functional characteristics.
Pub.: 07 Jan '17, Pinned: 26 Oct '17
Abstract: Tidal wetlands have been increasingly recognized as long-term carbon sinks in recent years. Work on carbon sequestration and decomposition processes in tidal wetlands focused so far mainly on effects of global-change factors such as sea-level rise and increasing temperatures. However, little is known about effects of land use, such as livestock grazing, on organic matter decomposition and ultimately carbon sequestration. The present work aims at understanding the mechanisms by which large herbivores can affect organic matter decomposition in tidal wetlands. This was achieved by studying both direct animal-microbe interactions and indirect animal-plant-microbe interactions in grazed and ungrazed areas of two long-term experimental field sites at the German North Sea coast. We assessed bacterial and fungal gene abundance using quantitative PCR, as well as the activity of microbial exo-enzymes by conducting fluorometric assays. We demonstrate that grazing can have a profound impact on the microbial community structure of tidal wetland soils, by consistently increasing the fungi-to-bacteria ratio by 38-42%, and therefore potentially exerts important control over carbon turnover and sequestration. The observed shift in the microbial community was primarily driven by organic matter source, with higher contributions of recalcitrant autochthonous (terrestrial) vs. easily degradable allochthonous (marine) sources in grazed areas favoring relative fungal abundance. We propose a novel and indirect form of animal-plant-microbe interaction: top-down control of aboveground vegetation structure determines the capacity of allochthonous organic matter trapping during flooding and thus the structure of the microbial community. Furthermore, our data provide the first evidence that grazing slows down microbial exo-enzyme activity and thus decomposition through changes in soil redox chemistry. Activities of enzymes involved in C cycling were reduced by 28-40%, while activities of enzymes involved in N cycling were not consistently affected by grazing. It remains unclear if this is a trampling-driven direct grazing effect, as hypothesized in earlier studies, or if the effect on redox chemistry is plant mediated and thus indirect. This study improves our process-level understanding of how grazing can affect the microbial ecology and biogeochemistry of semi-terrestrial ecosystems that may help explain and predict differences in C turnover and sequestration rates between grazed and ungrazed systems. This article is protected by copyright. All rights reserved.
Pub.: 21 Mar '17, Pinned: 26 Oct '17
Abstract: Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.
Pub.: 27 Jul '17, Pinned: 26 Oct '17
Abstract: Publication date: December 2016 Source:Soil Biology and Biochemistry, Volume 103 Author(s): Jennifer L. Wood, Caixian Tang, Ashley E. Franks Utilizing plants to remediate heavy metal contaminated soils, a process known as phytoextraction, offers many advantages but has yet to reach levels of efficiency that would make the strategy economically viable. Inoculation of the plant rhizosphere with microorganisms is an established route to improving phytoextraction efficiency. In general, microorganisms can improve phytoextraction by increasing the availability of heavy metals to the plant and by increasing plant biomass. This review uses a meta-analysis of the results from 103 microbial-augmented phytoextraction studies to examine if one of these microbial mechanisms has a greater potential to positively impact phytoextraction. Trends surrounding the use of heavy metal-accumulating versus non-heavy-metal-accumulating plants in phytoextraction are discussed. Microbially induced improvements in the accumulation of heavy metals in plant biomass, a focus of several studies, are always coincident with enhanced net phytoextraction. However, microbial treatments that improved plant biomass are more prevalent in the literature and account for a larger number of studies that reported improved phytoextraction, particularly in non-heavy-metal-accumulating plants. The experimental findings emerging from the literature that implicate specific microbial processes in improving phytoextraction are briefly reviewed and used to underline trends observed from the meta-analysis that indicate future directions regarding the use of microorganisms to improve phytoextraction efficiency.
Pub.: 28 Aug '16, Pinned: 26 Oct '17
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