Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems

Semënov, Mikhail; Krasnov, George S.; Семенов, В. М.; Bruggen, A.H.C. van

doi:10.1016/j.apsoil.2020.103641

Cited by 85 publications

(32 citation statements)

References 82 publications

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“…For example, soil microbiota is reported to increase in phylogenetic richness and community variability in organic systems (Lupatini et al, 2017), but this may be linked to the greater bioavailability of nutrient inputs in a more neutral soil pH (Lauber et al, 2009;Zhalina et al, 2015). Nutrient input, in particular, may be the driving force of these observations (Hartmann et al, 2015;Zhang et al, 2017;Semenov et al, 2020). There is also a knowledge gap of how soil microbial communities vary among contrasting organic systems.…”

Section: Introductionmentioning

confidence: 99%

Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

Ouverson

Eberly

Seipel

et al. 2021

Front. Sustain. Food Syst.

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Industrialized agriculture results in simplified landscapes where many of the regulatory ecosystem functions driven by soil biological and physicochemical characteristics have been hampered or replaced with intensive, synthetic inputs. To restore long-term agricultural sustainability and soil health, soil should function as both a resource and a complex ecosystem. In this study, we examined how cropping systems impact soil bacterial community diversity and composition, important indicators of soil ecosystem health. Soils from a representative cropping system in the semi-arid Northern Great Plains were collected in June and August of 2017 from the final phase of a 5-year crop rotation managed either with chemical inputs and no-tillage, as a USDA-certified organic tillage system, or as a USDA-certified organic sheep grazing system with reduced tillage intensity. DNA was extracted and sequenced for bacteria community analysis via 16S rRNA gene sequencing. Bacterial richness and diversity decreased in all farming systems from June to August and was lowest in the chemical no-tillage system, while evenness increased over the sampling period. Crop species identity did not affect bacterial richness, diversity, or evenness. Conventional no-till, organic tilled, and organic grazed management systems resulted in dissimilar microbial communities. Overall, cropping systems and seasonal changes had a greater effect on microbial community structure and diversity than crop identity. Future research should assess how the rhizobiome responds to the specific phases of a crop rotation, as differences in bulk soil microbial communities by crop identity were not detectable.

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Section: Introductionmentioning

confidence: 99%

Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

Ouverson

Eberly

Seipel

et al. 2021

Front. Sustain. Food Syst.

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“…It is suggested that there is an ecological relationship between Acidobacteria and Proteobacteria because they are often observed to be intimately associated (more often, negatively correlated) with each other in the environment, and may influence each other’s position in the community [ 54 ]. Alphaproteobacteria are considered as copiotrophs [ 55 , 56 ], while Acidobacteria are often considered as an oligotrophic group [ 54 , 55 ]. In addition, the presence of only one or two copies of 16S rRNA genes in the genomes of Acidobacteria was revealed, suggesting lower growth rates, which often correlates with oligotrophy [ 54 , 57 ].…”

Section: Discussionmentioning

confidence: 99%

“…The microbiome of the inlet zone was the most different from those in other zones of the CW and was characterized by the dominance of microbial genera belonging to the Sphingomonadaceae family: Sphingomonas, Sphingobium, Sphingopyxis, Novosphingobium, and Porphyrobacter. The representatives of Sphingomonadaceae are common inhabitants of soil and rhizosphere of plants [ 56 ]. Sphingomonadaceae can utilize hardly decomposable aromatic compounds, which makes these bacteria of interest to environmental remediation [ 59 ].…”

Section: Discussionmentioning

confidence: 99%

Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland

et al. 2020

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Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, one can expect the presence of distinct microbiomes across different CW zones. Here, we investigated spatial changes in microbiomes along different functional zones of a free-water surface wetland located in Moscow, Russia. The microbiome structure was analyzed using Illumina MiSeq amplicon sequencing. We also determined particle diameter and surface area of sediments, as well as chemical composition of organic pollutants in different CW zones. Specific organic particle aggregates similar to activated sludge flocs were identified in the sediments. The highest accumulation of hydrocarbons was found in the zones with predominant sedimentation of fine fractions. Phytofilters had the highest rate of organic pollutants decomposition and predominance of Smithella, Ignavibacterium, and Methanothrix. The sedimentation tank had lower microbial diversity, and higher relative abundances of Parcubacteria, Proteiniclasticum, and Macellibacteroides, as well as higher predicted abundances of genes related to methanogenesis and methanotrophy. Thus, spatial changes in microbiomes of constructed wetlands can be associated with different types of wastewater treatment processes.

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“…To overcome the low level of taxonomic capacity, high throughput sequencing based methods or metagenomic approaches have greatly enhanced our capability in measuring the totality of microbiomes, and almost all taxa can be detected and analyzed [ 135 , 136 , 137 , 138 , 139 , 140 ]. Sequence data are processed using bioinformatic analyses, which provides microbial diversity, abundance, and functional relationships.…”

Section: Measuring Soil Healthmentioning

confidence: 99%

Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production

Hao

Ashley

2021

Microorganisms

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Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress multiple soilborne pathogens. Soil amendments are naturally derived materials and products and can be classified into fresh or living plants, organic or inorganic matters, and microbial supplements. Fresh plants have unique functions and continuously exude chemicals to interact with soil microbes. Organic and inorganic matter contain high levels of nutrients, including nitrogen and carbon that plants and soil microorganisms need. Soil microorganisms, whether being artificially added or indigenously existing, are a key factor in plant health. Microbial communities can be considered as a biological reactor in an ecosystem, which suppress soilborne pathogens in various mechanisms and turn soil organic matter into absorbable forms for plants, regardless of amendment types. Therefore, soil amendments serve as an energy input, nutrient source, and a driving force of microbial activities. Advanced technologies, such as microbiome analyses, make it possible to analyze soil microbial communities and soil health. As research advances on mechanisms and functions, amendment-based strategies will play an important role in enhancing soil health and disease suppression for better potato production.

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Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems

Cited by 85 publications

References 82 publications

Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland

Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production

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