Soil microbial community dynamics and assembly under long-term land use change

Goss‐Souza, Dennis; Mendes, Lucas William; Borges, Clóvis Daniel; Baretta, Dilmar; Tsai, Siu Mui; Rodrigues, Jorge L. Mazza

doi:10.1093/femsec/fix109

Cited by 82 publications

(87 citation statements)

References 80 publications

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“…We used "metagenomeseq R package [46] to normalize the abundances. For details regarding DNA library preparation, sequencing procedure, and metagenome annotation see [27] (detailed information can also be found in Supplementary Material). Shotgun metagenome data are available at MG-RAST server under the project ID 7830.…”

Section: Sequencing and Bioinformaticsmentioning

confidence: 99%

“…Although selection could explain, in a certain way, the differences in microbial community assembly and diversifica-tion, empirical and theoretical models have shown that that not only selection but also drift and dispersal processes could be interacting with diversification [14], resulting in differential assembly patterns across soil types, soil fractions, time, and host plant species [25][26][27][28]. However, those processes have been often neglected in ecology studies.…”

mentioning

confidence: 99%

“…It can interact with selection and drift at the regional and local scales, modulating microbial dynamics [14]. Recently, emphasis has been given to the role of these processes on shaping microbial communities in dif-ferent ecosystems [13,18,25], such as agricultural soils [27] and the soilrhizosphere interface [7]. Evaluating microbial community assembly at the light of ecological processes could make it easier to have a comprehensive picture about the boundless amount of patterns arrangements [31] and the inter-play between deterministic and neutral processes governing those patterns [32,33].…”

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confidence: 99%

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Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

et al. 2019

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Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and,(ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

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Section: Sequencing and Bioinformaticsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

et al. 2019

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“…Also, belowground biodiversity loss is very likely to have negative effects both on the environment and on the sustainability of agricultural production as microbial functions will be altered (Tardy et al, 2014). Recently, metagenomic approaches have investigated the impact on the composition and structure of soil microbiome of converting semi-deciduous Amazonian rainforest and natural grasslands to arable soils (Mendes et al, 2015;Castañeda and Barbosa, 2017;Goss-Souza et al, 2017;Kroeger et al, 2018). These studies found that arable soils were similar or more diverse than the original ecosystem and that functional redundancy overcomes the ecosystem transformation.…”

Section: Discussionmentioning

confidence: 99%

Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey

Muñoz-Arenas

Fusaro

Hernández‐Guzmán

et al. 2020

Environ Microbiol Rep

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Summary Land‐use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high‐altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high‐altitude temperate oak and pine‐oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land‐use change. Archaea diversity was not affected by land‐use change, but the bacterial diversity decreased with 45–55% when the oak forest was converted to arable land and 65–75% when the pine‐oak forest was. Loss in bacterial diversity as a result of land‐use change was positively correlated (R2 = 0.41) with the 10–25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land‐use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine‐oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity.

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“…Taken together, we provide new evidence that low-disturbance practice promotes deep-soil stability to cope with environmental stress through increasing water and nutrient holding capacity, microbial richness, microbial diversity and ecological functions. According to ecological theory(49, 50), microbial community assembly in the CT treatment was mainly based on deterministic processes and significantly influenced by environmental stress and fertilizer nitrogen. Stover mulching might alter these processes through deeper roots affecting the vertical heterogeneity in resource availability(4).…”

Section: Discussionmentioning

confidence: 99%

Low-disturbance Farming Regenerates Healthy Deep Soil towards Sustainable Agriculture

Deng

Wang

Xie

et al. 2019

Preprint

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SummaryIntensive conventional farming has degraded farmland topsoil and seriously threaten food and environment security globally. Although low-disturbance practices have been widely adapted to restore soil health, whether this measure in a long run can potentially recover the critical deep soil to meet sustainable intensification of crop production are still unclear. Here we compared soil microbiome, physiochemical parameters along 3-m deep soil profiles, and crop yield in Northeast China subjected to ten years of farming practices at 3 levels of disturbance, including conventional tillage (CT), no-tillage without stover mulching (NTNS), and no-tillage with stover mulching (NTSM). We found that low-disturbance practices (NTNS and NTSM) promoted the ability of the deep soil to retain water and nitrogen, regenerated whole-soil microbial diversity and function, and significantly improved corn yield in the drought year. This study implies that the low-disturbance practices could dig deeper for agricultural resource and reduce energy consumption and greenhouse gas emissions, thus regenerating highly efficient, sustainable agriculture.Science for SocietyBy 2050, how to feed 10 billion people on limited land without destroying the environment has become a global challenge. Prior research has shown that low-disturbance farming enhances biodiversity and natural biological processes in farmland topsoil, which benefit crop production. However, whether long-term low-disturbance farming could regenerate deep-soil health to meet sustainable intensification of crop production remains unclear. We evaluate the impact of low-disturbance practices on 3-meter soil profile after 10-year manipulations and provide an underneath mechanism on how long-term low-disturbance farming regenerate deep healthy soil. We found that low-disturbance farming not only promoted soil nutrient and water holding capacities, restored microbial diversity, richness, and ecological function in the whole 3-m soil profile, but also improved crop production (especially during drought) and potentially reduced energy consumption and greenhouse gas emissions, thus promoting sustainable agriculture and ensuring food and environment security.Graphical Abstract

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Soil microbial community dynamics and assembly under long-term land use change

Cited by 82 publications

References 80 publications

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey

Low-disturbance Farming Regenerates Healthy Deep Soil towards Sustainable Agriculture

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