Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil ...biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.
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NUK, SBMB, SBNM, UL, UM, UPUK
Wastewater, tourism, and trade are moving microbes around the globe at an unprecedented scale
For several billion years, microorganisms and the genes they carry have mainly been moved by physical ...forces such as air and water currents. These forces generated biogeographic patterns for microorganisms that are similar to those of animals and plants (
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). In the past 100 years, humans have changed these dynamics by transporting large numbers of cells to new locations through waste disposal, tourism, and global transport and by modifying selection pressures at those locations. As a consequence, we are in the midst of a substantial alteration to microbial biogeography. This has the potential to change ecosystem services and biogeochemistry in unpredictable ways.
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BFBNIB, NMLJ, NUK, ODKLJ, PNG, SAZU, UL, UM, UPUK
In addition to changes in climate, land cover, biodiversity, and chemical composition, human activity is also inducing great changes in the microbial world. These changes are profoundly affecting the ...biogeochemical processes of the Earth, the global biology, and the human health, that is, they are influencing the sustainability of the Anthropocene.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Antibiotic resistance is a global health crisis linked to increased, and often unrestricted, antibiotic use in humans and animals. As one of the world's largest producers and consumers of ...antibiotics, China is witness to some of the most acute symptoms of this crisis. Antibiotics and antibiotic resistance genes (ARGs) are widely distributed in surface water, sewage treatment plant effluent, soils and animal wastes. The emergence and increased prevalence of ARGs in the clinic/hospitals, especially carbapenem-resistant gram negative bacteria, has raised the concern of public health officials. It is important to understand the current state of antibiotic use in China and its relationship to ARG prevalence and diversity in the environment. Here we review these relationships and their relevance to antimicrobial resistance (AMR) trends witnessed in the clinical setting. This review highlights the issues of enrichment and dissemination of ARGs in the environment, and also future needs in mitigating the spread of antibiotic resistance in the environment, particularly under the ‘planetary health’ perspective, i.e., the systems that sustain or threaten human health.
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•Antibiotics and ARGs are widely distributed in environment media in China.•Antibiotic resistance varies geographically in China.•Strategies to mitigate the spread of antibiotic resistance are suggested.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Microplastics are emerging pollutants that have recently aroused considerable concern but most toxicological studies have focused on marine biota, with little investigation of the influence of ...microplastics on terrestrial ecosystems. Here, we fed the soil oligochaete Enchytraeus crypticus with oatmeal containing 0, 0.025, 0.5, and 10% (dry weight basis) nano-polystyrene (0.05–0.1 μm particle size) to elucidate the impact of microplastics on the growth and gut microbiome of Enchytraeus crypticus. We observed a significant reduction of weight in the animals fed 10% polystyrene and an increase in the reproduction of those fed 0.025%. More importantly, using 16S rRNA amplification and high-throughput sequencing we found a significant shift in the microbiome of those fed 10% microplastics with significant decreases in the relative abundance of the families Rhizobiaceae, Xanthobacteraceae and Isosphaeraceae. These families contain key microbes that contribute to nitrogen cycling and organic matter decomposition.
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•Exposure to nano-polystyrene disrupted the Enchytraeus crypticus microbiome.•Nano-polystyrene led to a decrease in bacterial diversity and a structural shift.•Exposure to nano-polystyrene altered the weight and reproduction of E. crypticus.
Nano-polystyrene exposure disrupted the microbiome of Enchytraeus crypticus, leading to a decrease in microbial diversity and a structural shift in bacterial composition.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials ...are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.
In this paper, we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The demand for organic food products, especially for organic vegetables has been growing rapidly in the last few decades. However, the risk of introducing more antibiotic resistant genes (ARGs) and ...antibiotic resistant bacteria (ARB) to the vegetables by organic production procedures has long been overlooked. In our study, by using high-throughput quantitative PCR and 16sRNA Illumina sequencing technology, we investigated the abundance and diversity of ARGs and the microbial communities in conventionally (CPL) and organically produced lettuce (OPL). A total of 134 ARGs were detected in the phyllosphere and leaf endophyte of the samples. Absolute copy numbers of ARGs in phyllosphere were 8-fold higher in the OPL than in CPL. We also observed a significant difference in the microbial communities between OPL and CPL, and a lower diversity of both phyllosphere and leaf endophytic bacteria in OPL than in CPL. The Mantel test and variation partitioning analysis (VPA) suggested that the profile of ARGs is strongly affected by bacterial community compositions. Network analysis between ARGs and bacterial taxa indicated that eight bacterial families were implicated to be the potential hosts of ARGs. These results provide insights into the impacts of organic farming on the profiles of bacterial and ARG compositions in vegetables.
•Organically produced lettuce harbors higher abundance and diversity of ARGs than conventionally produced.•HT-qPCR is an effective approach to investigate the ARGs in environmental samples.•Bacterial community shifts, is the major driver shaping the antibiotic resistome in vegetables.•Network analysis can provide new insights into ARGs and their possible hosts in complex environmental scenarios.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Summary
Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known.
Here we examined bacterial communities ...across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)‐wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites.
Our results demonstrate that microbiome assembly along the soil‐plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize.
Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Since the introduction of antibiotics into clinical practices in the 1940s, antibiotics have become an integral part of animal production to meet the increasing human demand for animal-derived foods. ...As a result, industrial-scale animal production has emerged as a hotspot for the evolution and dissemination of antibiotic resistance genes (ARGs), thereby potentially contributing to a looming public health crisis. The knowledge of ARGs in livestock systems has been greatly expanded with the recent development of rapid molecular tools. However, comprehensive reviews on ARGs in the animal industry and possible mitigation solutions are still lacking from a One Health perspective. Here we provide this review focusing on human health risks associated with the antimicrobial (antibiotic and metal) usages, ARGs in livestock animals and aquaculture systems in a One Health perspective to untangle the complexities of ARGs across animals, environments and humans. Specifically, this review covers (1) antimicrobials usages in the animal industry, (2) ARGs in animals affected by selective agents, (3) animal-to-human direct/indirect ARG transmission pathways, and (4) mitigation approaches. We highlighted the burden of using antimicrobials in animals for public and environmental health, and also the urgent needs for mitigating the spread of antibiotic resistance from the livestock and aquaculture industries.
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BFBNIB, GIS, IJS, KISLJ, NUK, PNG, UL, UM, UPUK
•We built a correlation network using fungal and bacterial taxa.•Kinless hubs were highly positively correlated with the abundance of functional genes.•SEM results highlighted the positive effect of ...kinless hubs on the functional genes.
Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of the role of kinless hubs in regulating the functional potential of soil microbial communities, however, is largely unexplored and poorly understood in agricultural ecosystems. Here, we built a correlation network of fungal and bacterial taxa using a large-scale survey consisting of 243 soil samples across functionally and economically important agricultural ecosystems (wheat and maize); and found that the relative abundance of taxa classified as kinless hubs within the ecological network are positively and significantly correlated with the abundance of functional genes including genes for C fixation, C degradation, C methanol, N cycling, P cycling and S cycling. Structural equation modeling of multiple soil properties further indicated that kinless hubs, but not provincial, connector or peripheral taxa, had direct significant and positive relationships with the abundance of multiple functional genes. Our findings provide novel evidence that the relative abundance of soil taxa classified as kinless hubs within microbial networks are associated with high functional potential, with implications for understanding and managing (through manipulating microbial key species) agricultural ecosystems at a large spatial scale.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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