Adding alfalfa to an annual crop rotation shifts the composition and functional responses of tomato rhizosphere microbial communities

2021 ◽  
Vol 167 ◽  
pp. 104102
Author(s):  
Sandipan Samaddar ◽  
Radomir Schmidt ◽  
Nicole E. Tautges ◽  
Kate Scow
2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
A. Marais ◽  
M. Hardy ◽  
M. Booyse ◽  
A. Botha

Different plants are known to have different soil microbial communities associated with them. Agricultural management practices such as fertiliser and pesticide addition, crop rotation, and grazing animals can lead to different microbial communities in the associated agricultural soils. Soil dilution plates, most-probable-number (MPN), community level physiological profiling (CLPP), and buried slide technique as well as some measured soil physicochemical parameters were used to determine changes during the growing season in the ecosystem profile in wheat fields subjected to wheat monoculture or wheat in annual rotation with medic/clover pasture. Statistical analyses showed that soil moisture had an over-riding effect on seasonal fluctuations in soil physicochemical and microbial populations. While within season soil microbial activity could be differentiated between wheat fields under rotational and monoculture management, these differences were not significant.


2008 ◽  
Vol 127 (3-4) ◽  
pp. 286-293 ◽  
Author(s):  
Pierre Plassart ◽  
Marthe Akpa Vinceslas ◽  
Christophe Gangneux ◽  
Anne Mercier ◽  
Sylvie Barray ◽  
...  

2017 ◽  
Vol 419 (1-2) ◽  
pp. 435-445 ◽  
Author(s):  
Björn Breidenbach ◽  
Kristof Brenzinger ◽  
Franziska B. Brandt ◽  
Martin B. Blaser ◽  
Ralf Conrad

2016 ◽  
Vol 82 (9) ◽  
pp. 2862-2871 ◽  
Author(s):  
Christopher J. Graves ◽  
Elizabeth J. Makrides ◽  
Victor T. Schmidt ◽  
Anne E. Giblin ◽  
Zoe G. Cardon ◽  
...  

ABSTRACTEnvironmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.IMPORTANCEIn this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.


2016 ◽  
Vol 80 ◽  
pp. 88-104 ◽  
Author(s):  
Carlos A.C. Crusciol ◽  
Rubia R. Marques ◽  
Antonio C.A. Carmeis Filho ◽  
Rogério P. Soratto ◽  
Claudio H.M. Costa ◽  
...  

2021 ◽  
Vol 5 ◽  
Author(s):  
Tindall Ouverson ◽  
Jed Eberly ◽  
Tim Seipel ◽  
Fabian D. Menalled ◽  
Suzanne L. Ishaq

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.


2017 ◽  
Vol 26 (1) ◽  
pp. 39-46 ◽  
Author(s):  
Anna Gałązka ◽  
Karolina Gawyjołek ◽  
Andrzej Perzyński ◽  
Rafał Gałązka ◽  
Księżak Jerzy

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qi Qi ◽  
Yue Haowei ◽  
Zhenhua Zhang ◽  
Joy D. Van Nostrand ◽  
Linwei Wu ◽  
...  

ABSTRACT Soil microorganisms are sensitive to temperature in cold ecosystems, but it remains unclear how microbial responses are modulated by other important climate drivers, such as precipitation changes. Here, we examine the effects of six in situ warming and/or precipitation treatments in alpine grasslands on microbial communities, plants, and soil carbon fluxes. These treatments differentially affected soil carbon fluxes, gross primary production, and microbial communities. Variations of soil CO2 and CH4 fluxes across all sites significantly (r > 0.70, P < 0.050) correlated with relevant microbial functional abundances but not bacterial or fungal abundances. Given tight linkages between microbial functional traits and ecosystem functionality, we conclude that future soil carbon fluxes in alpine grasslands can be predicted by microbial carbon-degrading capacities. IMPORTANCE The warming pace in the Tibetan Plateau, which is predominantly occupied by grassland ecosystems, has been 0.2°C per decade in recent years, dwarfing the rate of global warming by a factor of 2. Many Earth system models project substantial carbon sequestration in Tibet, which has been observed. Here, we analyzed microbial communities under projected climate changes by 2100. As the soil “carbon pump,” the growth and activity of microorganisms can largely influence soil carbon dynamics. However, microbial gene response to future climate scenarios is still obscure. We showed that the abundances of microbial functional genes, but not microbial taxonomy, were correlated with carbon fluxes and ecosystem multifunctionality. By identifying microbial traits linking to ecosystem functioning, our results can guide the assessment of future soil carbon fluxes in alpine grasslands, a critical step toward mitigating climate changes.


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