Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation

ABSTRACT Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties and plant and microbial communities, in particular, on microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C 4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. With less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38% to 137% in response to either clipping or the combined treatment, which could weaken long-term soil carbon stability and trigger positive feedback with respect to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization, and denitrification by 32% to 39%. Such potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium levels caused by clipping alone and could contribute to unchanged plant biomass levels. Moreover, clipping tended to interact antagonistically with warming, especially with respect to effects on nitrogen cycling genes, demonstrating that single-factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties as well as the abundance and structure of soil microbial functional genes. Aboveground biomass removal for biofuel production needs to be reconsidered, as the long-term soil carbon stability may be weakened. IMPORTANCE Global change involves simultaneous alterations, including those caused by climate warming and land management practices (e.g., clipping). Data on the interactive effects of warming and clipping on ecosystems remain elusive, particularly in microbial ecology. This study found that clipping alters microbial responses to warming and demonstrated the effects of antagonistic interactions between clipping and warming on microbial functional genes. Clipping alone or combined with warming enriched genes degrading relatively recalcitrant carbon, likely reflecting the decreased quantity of soil carbon input from litter, which could weaken long-term soil C stability and trigger positive warming feedback. These results have important implications in assessing and predicting the consequences of global climate change and indicate that the removal of aboveground biomass for biofuel production may need to be reconsidered.

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Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

Microorganisms ◽

10.3390/microorganisms9071400 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1400

Author(s):

Marta Bertola ◽

Andrea Ferrarini ◽

Giovanna Visioli

Keyword(s):

Microbial Diversity ◽

Food Quality ◽

Plant Biomass ◽

Soil Microbial Communities ◽

Well Being ◽

Plant Health ◽

Soil Microbiome ◽

Soil Microbial Diversity ◽

Soil Biodiversity ◽

Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

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Can repeated soil amendment with biogas digestates increase soil suppressiveness toward non-specific soil-borne pathogens in agricultural lands?

Renewable Agriculture and Food Systems ◽

10.1017/s1742170520000393 ◽

2020 ◽

pp. 1-12

Author(s):

L. M. Manici ◽

F. Caputo ◽

G. A. Cappelli ◽

E. Ceotto

Keyword(s):

Plant Growth ◽

Biomass Production ◽

Soil Amendment ◽

Plant Biomass ◽

Amended Soils ◽

Soil Suppressiveness ◽

Soil Microbial ◽

Soil Borne Pathogens ◽

The Impact ◽

Plant Biomass Production

Abstract Soil suppressiveness which is the natural ability of soil to support optimal plant growth and health is the resultant of multiple soil microbial components; which implies many difficulties when estimating this soil condition. Microbial benefits for plant health from repeated digestate applications were assessed in three experimental sites surrounding anaerobic biogas plants in an intensively cultivated area of northern Italy. A 2-yr trial was performed in 2017 and 2018 by performing an in-pot plant growth assay, using soil samples taken from two fields for each experimental site, of which one had been repeatedly amended with anaerobic biogas digestate and the other had not. These fields were similar in management and crop sequences (maize was the recurrent crop) for the last 10 yr. Plant growth response in the bioassay was expressed as plant biomass production, root colonization frequency by soil-borne fungi were estimated to evaluate the impact of soil-borne pathogens on plant growth, abundance of Pseudomonas and actinomycetes populations in rhizosphere were estimated as beneficial soil microbial indicators. Repeated soil amendment with digestate increased significantly soil capacity to support plant biomass production as compared to unamended control in both the years. Findings supported evidence that this increase was principally attributable to a higher natural ability of digestate-amended soils to reduce root infection by saprophytic soil-borne pathogens whose inoculum was increased by the recurrent maize cultivation. Pseudomonas and actinomycetes were always more abundant in digestate-amended soils suggesting that both these large bacterial groups were involved in the increase of their natural capacity to control soil-borne pathogens (soil suppressiveness).

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Soil amendments alter plant biomass and soil microbial activity in a semi-desert grassland

Plant and Soil ◽

10.1007/s11104-017-3327-5 ◽

2017 ◽

Vol 419 (1-2) ◽

pp. 53-70 ◽

Cited By ~ 12

Author(s):

Martha Gebhardt ◽

Jeffrey S. Fehmi ◽

Craig Rasmussen ◽

Rachel E. Gallery

Keyword(s):

Microbial Activity ◽

Plant Biomass ◽

Soil Amendments ◽

Soil Microbial Activity ◽

Desert Grassland ◽

Soil Microbial

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Early Spring Snowmelt and Summer Droughts Strongly Impair the Resilience of Key Microbial Communities in Subalpine Grassland Ecosystems

10.1101/2021.03.15.435477 ◽

2021 ◽

Author(s):

Farhan Hafeez ◽

Lionel Bernard ◽

Jean-Christophe Clement ◽

Franck Poly ◽

Thomas Pommier

Keyword(s):

Microbial Communities ◽

Plant Biomass ◽

Early Spring ◽

Climatic Extremes ◽

Soil Microbial ◽

Cascading Effect ◽

Growing Seasons ◽

Grassland Ecosystems ◽

Microbial Responses ◽

Early Snowmelt

Subalpine grassland ecosystems are important from biodiversity, agriculture, and touristic perspectives but their resilience to seasonally occurring climatic extremes is increasingly challenged with climate change, accelerating their vulnerability to tipping points. Microbial communities, which are central in ecosystem functioning, are usually considered as more resistant and highly resilient to such extreme events due to their functional redundancy and strong selection in residing habitats. To investigate this, we explored the soil microbial responses upon recurrent summer droughts associated with early snowmelt in grasslands mesocosms set-up at the Lautaret Pass (French Alps). Potential respiration, nitrification and denitrification were monitored over a period of two growing seasons along with quantification of community gene abundances of total bacteria as well as (de)nitrifiers. Results revealed that droughts had a low and short-term impact on bacterial total respiration supporting their hypothesized high resistance and ability to recover. Nitrification and abundances of the corresponding functional guilds showed relatively strong resistance to summer droughts but declined in response to early snowmelt. This triggered a cascading effect on denitrification but also on the abundances of denitrifying communities which could recover from all climatic extremes except from the summer droughts where nitrifiers were collapsed. Denitrification and the respective functional groups faced high impact of applied stresses with strong reduction in the abundance and activity of this specialized community. Although, the consequently lower microbial competition for nitrate may be positive for plant biomass production, warnings exist when considering the potential nitrogen leaching from these ecosystems as well as risks of greenhouses gases emission such as N2O

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Agricultural practice negatively affects soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

10.22541/au.163705519.94774515/v2 ◽

2021 ◽

Author(s):

Tiehang Wu ◽

Michael Sabula ◽

Holli Milner ◽

Gary Strickland ◽

Gan Liu

Keyword(s):

Community Structure ◽

Bacterial Diversity ◽

Forest Soils ◽

Agricultural Practices ◽

Functional Genes ◽

Agricultural Practice ◽

Soil Bacterial Diversity ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

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Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

Frontiers in Microbiology ◽

10.3389/fmicb.2016.00060 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 38

Author(s):

Yuting Liang ◽

Huihui Zhao ◽

Ye Deng ◽

Jizhong Zhou ◽

Guanghe Li ◽

...

Keyword(s):

Ecological Networks ◽

Functional Genes ◽

Oil Contamination ◽

Soil Microbial

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Effects of biochar on soil microbial community and functional genes of a landfill cover three years after ecological restoration

The Science of The Total Environment ◽

10.1016/j.scitotenv.2020.137133 ◽

2020 ◽

Vol 717 ◽

pp. 137133 ◽

Cited By ~ 4

Author(s):

Hang Lu ◽

Mengxue Yan ◽

Ming Hung Wong ◽

Wing Yin Mo ◽

Yinghui Wang ◽

...

Keyword(s):

Microbial Community ◽

Ecological Restoration ◽

Soil Microbial Community ◽

Functional Genes ◽

Soil Microbial ◽

Landfill Cover

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Soil Organic Carbon Chemical Functional Groups under Different Revegetation Types Are Coupled with Changes in the Microbial Community Composition and the Functional Genes

Forests ◽

10.3390/f10030240 ◽

2019 ◽

Vol 10 (3) ◽

pp. 240 ◽

Cited By ~ 3

Author(s):

Jiaojiao Deng ◽

Wenxu Zhu ◽

Yongbin Zhou ◽

You Yin

Keyword(s):

Microbial Community ◽

Chemical Composition ◽

Organic Carbon ◽

Functional Groups ◽

Soil Microbial Community ◽

Coniferous Forests ◽

Functional Genes ◽

Broadleaf Forest ◽

Soil Microbial ◽

Molecular Compounds

Different revegetatiom types can affect the chemical composition of soil organic carbon (SOC), soil microbial community and the functional genes related to carbon cycle. However, the relationships between SOC chemical functional groups and soil microbial communities and the functional genes remains poorly unclear under different revegetation types. Using the solid-state 13C nuclear magnetic resonance (NMR) spectroscopy, we examined changes in the SOC chemical composition of five soils (0–10 cm depth) from Larix gmelinii Rupr. (LG), Pinus koraiensis Sieb. (PK), Quercus mongolica Fisch. (QM), Juglans mandshurica Maxim. (JM), and conifer-broadleaf forest (CB). And the soil microbial community genes related to metabolism of macro-molecular compounds were determined via whole genome shotgun based on Illumina HiSeq. Our results indicated that broadleaf forests (JM, QM) had increased the contents of soil total carbon (C), total nitrogen (N), dissolved organic carbon (DOC), and microbial biomass carbon (MBC), compared with coniferous forests (LG, PK) and the conifer-broadleaf forest (CB). While, the coniferous forests generated a lower O-alcoxyl C, a higher alkyl C, and the ratio of alkyl C/O-alkyl C than broadleaf forests. A total of four kingdoms were identified via whole metagenome shotgun sequencing, including eight archaea, 55 bacteria, 15 eukaryota, and two viruses, giving a total 80 phyla. The contents of alkyne C, phenolic C, methoxyl C, COO/NC=O, and alkyl C were strong related to the composition of soil microbial community and their contents illuminated a major part of the variation in soil microbial composition. We detected seven corresponding macro-molecular compounds of different organic carbon functional group, and 244 genes related to metabolism across all samples, and soil total C, total N, and DOC could be the main factors for microbial functional gene composition. Interestingly, the relative abundances of different SOC chemical functional groups, the phylogenetic distance for microbes, the genes of C cycling based on the KEGG database, and the relative abundance of genes related to metabolism of macro-molecular compounds of different SOC chemical functional groups under different revegetation types all could be divided into three groups, including PK plus LG, JM plus QM, and CB. Our results also illustrated that variations in SOC chemical functional groups were strongly associated with changes of soil microbial community taxa and functional genes, which might be affected by the changes of soil characteristics.

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