School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemPlant and soil biodiversity is essential for supporting highly multifunctional forests during Mediterranean rewilding(Wiley, 2023-02-01)1. The multidimensional dynamics of biodiversity and ecosystem function during the rewilding of Mediterranean forests remain poorly understood, limiting our capacity to predict how future restoration efforts may help mitigate climate change. 2. Here, we investigated the changes in multiple dimensions of biodiversity and ecosystem services in a 120-year forest succession after harvest to identify potential trade-offs in multiple dimensions of ecosystem function, and further assess the link between above and below-ground biodiversity and function. 3. We found a positive influence of successional age on not only multiple dimensions of biodiversity and function but also some important trade-offs. Two ecosystem axes of function explained nearly 75.4% of functional variation during ecosystem rewilding. However, while the first axis increased with successional age promoting plant productivity and element stocks, the second axis followed a hump-shaped relationship with age supporting important reductions in nutrient availability and pathogen control in old forests. Our study further revealed a significant positive relationship between plant and soil biodiversity with multiple elements of multifunctionality as forests develop. Moreover, the influence of plant and soil biodiversity were especially important to support a high number of function working at high levels of functioning. 4. Our work provides new insights on the patterns and functional trade-offs in the multidimensional rewilding of forests and further highlights the importance of biodiversity for long-term Mediterranean rewilding.
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ItemPrecipitation seasonality and soil pH drive the large-scale distribution of soil invertebrate communities in agricultural ecosystems(OXFORD UNIV PRESS, 2023-10-17)Soil invertebrates contribute significantly to vital ecosystem functions such as the breakdown of organic matter and cycling of essential nutrients, but our knowledge of their large-scale distribution in agricultural systems is limited, which hinders our ability to robustly predict how they will respond to future global change scenarios. Here, we employed metabarcoding analysis of eukaryotic 18S rRNA genes to examine the diversity and community composition of invertebrates in 528 sorghum rhizosphere and bulk soils, collected from 53 experimental field sites across China. Our results revealed that Nematoda, Arthropoda and Annelida were the dominant soil invertebrate groups in agroecosystems. Among all the climatic and soil parameters we examined, precipitation seasonality (i.e. the irregular distribution of precipitation during a normal year) had the strongest relationship with the richness of soil invertebrates, with an increase in soil invertebrate richness predicted with increasing precipitation seasonality. Mean annual precipitation and soil pH were the most important predictors of soil invertebrate community structure, with numerous invertebrate phylotypes showing either significantly positive or negative relationships with these two variables. Our findings suggest that shifts in precipitation patterns and soil pH, induced by future climate change and agricultural practices, will have important consequences for the distribution of soil invertebrate communities, with implications for agricultural ecosystem sustainability.
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ItemProtistan predation selects for antibiotic resistance in soil bacterial communities(Oxford University Press, 2023-12)Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJ and ttgB genes) and tetracycline (tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.
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ItemDistinct kin strategies of the legume soybean and the non-legume balsam by accomplishing different nitrogen acquisition and rhizosphere microbiome composition(WILEY, 2022-04)SUMMARY Kin selection has been proposed vvto be an important mechanism for plant relatives growing together. To reveal kin recognition, we used 15N labeling to assess the short‐term nitrogen (N) acquisition (uptake of nitrate and ammonium), long‐term N utilization (recovery of added urea), N‐use efficiency (NUE) and rhizosphere microbiome in leguminous Glycine max and non‐leguminous Impatiens balsamina. Individuals of each species were planted pairwise with either a sibling or a stranger. Enzyme activity and soil microbial composition were compared between kinship groups. Compared with strangers, G. max siblings increased aboveground biomass, NUE, and nitrogenase activity, whereas I. balsamina siblings decreased root biomass and increased uptake rate of nitrate and potential nitrification rate. Plant kinship affected soil bacterial communities by enriching specific groups possessing explicit eco‐functions (Rhizobiales for G. max and Nitrospira for I. balsamina). Kinship‐sensitive operational taxonomic units formed independent modules in the bacterial co‐occurrence network and were positively correlated with plant growth performance, N acquisition and enzymatic activity. Plant kin recognition may depend on the growth strategies of the plant species. Kin selection was dominant in G. max by enhancing biological N fixation through the enrichment of symbiotic rhizobia (demonstrated by aboveground growth and NUE superiority among siblings). Kin selection and niche partitioning occurred simultaneously in I. balsamina, expressed through reduced root allocation but increased nitrate uptake, and enhanced soil N nitrification, by enriching functional microbial groups. Kin recognition responses are the consequence of complex interactions among the host plant, the microbiome, and soil nutrient cycling and utilization processes.
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ItemNo Preview AvailableTrophic interrelationships of bacteria are important for shaping soil protist communities(WILEY, 2023-08)Protists occupy multiple trophic positions in soil food webs and significantly contribute to organic matter decomposition and biogeochemical cycling. Protists can ingest bacteria and fungi as main food sources while being subjected to predation of invertebrates, but our understanding of how bottom-up and top-down regulations structure protists in natural soil habitats is limited. Here, we disentangle the effects of trophic regulations to the diversity and structure of soil protists in natural settings across northern and eastern Australia. Bacterial and invertebrate diversity were identified as important drivers of the diversity of functional groups of protists. Moreover, the compositions of protistan taxonomic and functional groups were better predicted by bacteria and fungi, than by soil invertebrates. There were strong trophic interconnections between protists and bacteria in multiple organismic network analysis. Altogether, the study provided new evidence that, bottom-up control of bacteria played an important role in shaping the soil protist community structure, which can be derived from feeding preferences of protists on microbial prey, and their intimate relationships in soil functioning or environmental adaptation. Our findings advance our knowledge about the impacts of different trophic groups on key soil organismic communities, with implications for ecosystem functions and services.
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ItemNo Preview AvailableCross-biome antibiotic resistance decays after millions of years of soil development(SPRINGERNATURE, 2022-07)Soils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments.
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ItemNo Preview AvailableCalling for comprehensive explorations between soil invertebrates and arbuscular mycorrhizas(CELL PRESS, 2022-08)Arbuscular mycorrhizal (AM) fungi and soil invertebrates represent a large proportion of total soil biomass and biodiversity and are vital for plant performance, soil structure, and biogeochemical cycling. However, the role of soil invertebrates in AM fungi development remains elusive. In this opinion article, we summarize the ecological importance of AM fungi and soil invertebrates in the plant-soil continuum and highlight the effects of soil invertebrates on AM fungal hyphae development and functioning. In a context of global change, we envision that better mechanistic understanding of the complex feedback via chemical signaling pathways across the interactions between soil invertebrates and AM fungi is critical to predict their ecological consequences and will open new avenues for promoting ecosystem resilience and sustainability.
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ItemNo Preview AvailableAridity decreases soil protistan network complexity and stability(PERGAMON-ELSEVIER SCIENCE LTD, 2022-03)
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ItemNo Preview AvailableCross-biome soil viruses as an important reservoir of virulence genes(ELSEVIER, 2023-01-15)Viruses can significantly influence the composition and functions of their host communities and enhance host pathogenicity via the transport of virus-encoded virulence genes. However, the contribution of viral communities to the dissemination of virulence genes across various biomes across a large scale is largely unknown. Here, we constructed 29,283 soil viral contigs (SVCs) from viral size fraction metagenomes and public databases. A total of 1310 virulence genes were identified from 1164 SVCs in a wide variety of soil biomes, including grassland, agricultural and forest soils. The virulence gene gmd was the most abundant one, followed by csrA, evpJ, and pblA. A great proportion of viruses encoding virulence genes were uncharacterized. Virus-host linkage analysis revealed that most viruses were linked to only one bacterial genus, whereas several SVCs were associated with more than one bacterial genus and even two bacterial phyla, suggesting the potential risk of spreading virulence genes across different bacterial communities via viruses. Altogether, we provided new evidence for the prevalence of virulence genes in soil viruses across biomes, which advanced our understanding of the potential role of soil viruses in driving the pathogenesis of their hosts in terrestrial ecosystems.