Functional and molecular responses of soil microbial communities under differing soil management practices

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.

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Continuous monocropping highly affect the composition and diversity of microbial communities in peanut (Arachis hypogaea L.)

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha49412532 ◽

2021 ◽

Vol 49 (4) ◽

pp. 12532

Author(s):

Ali I. MALLANO ◽

Xianli ZHAO ◽

Yanling SUN ◽

Guangpin JIANG ◽

Huang CHAO

Keyword(s):

Microbial Communities ◽

Management Practices ◽

Rhizosphere Soil ◽

Diversity Index ◽

Cropping Systems ◽

Soil Microbial Communities ◽

Pathogenic Fungi ◽

Continuous Cropping ◽

Bacterial Phyla ◽

Soil Microbial

Continuous cropping systems are the leading cause of decreased soil biological environments in terms of unstable microbial population and diversity index. Nonetheless, their responses to consecutive peanut monocropping cycles have not been thoroughly investigated. In this study, the structure and abundance of microbial communities were characterized using pyrosequencing-based approach in peanut monocropping cycles for three consecutive years. The results showed that continuous peanut cultivation led to a substantial decrease in soil microbial abundance and diversity from initial cropping cycle (T1) to later cropping cycle (T3). Peanut rhizosphere soil had Actinobacteria, Protobacteria, and Gemmatimonadetes as the major bacterial phyla. Ascomycota, Basidiomycota were the major fungal phylum, while Crenarchaeota and Euryarchaeota were the most dominant phyla of archaea. Several bacterial, fungal and archaeal taxa were significantly changed in abundance under continuous peanut cultivation. Bacterial orders, Actinomycetales, Rhodospirillales and Sphingomonadales showed decreasing trends from T1>T2>T3. While, pathogenic fungi Phoma was increased and beneficial fungal taxa Glomeraceae decreased under continuous monocropping. Moreover, Archaeal order Nitrososphaerales observed less abundant in first two cycles (T1&T2), however, it increased in third cycle (T3), whereas, Thermoplasmata exhibit decreased trends throughout consecutive monocropping. Taken together, we have shown the taxonomic profiles of peanut rhizosphere communities that were affected by continuous peanut monocropping. The results obtained from this study pave ways towards a better understanding of the peanut rhizosphere soil microbial communities in response to continuous cropping cycles, which could be used as bioindicator to monitor soil quality, plant health and land management practices.

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Season and soil management affect soil microbial communities estimated using phospholipid fatty acid analysis in a continuous cabbage (Brassica oleraceavar.capitata) cropping system

Soil Science & Plant Nutrition ◽

10.1111/j.1747-0765.2008.00242.x ◽

2008 ◽

Vol 54 (3) ◽

pp. 369-378 ◽

Cited By ~ 11

Author(s):

Hiroyasu Tabuchi ◽

Kotaro Kato ◽

Ichio Nioh

Keyword(s):

Fatty Acid ◽

Microbial Communities ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Cropping System ◽

Soil Management ◽

Fatty Acid Analysis ◽

Phospholipid Fatty Acid Analysis ◽

Soil Microbial

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Responses of Bacterial and Fungal Community Structure to Different Rates of 1,3-Dichloropropene Fumigation

Phytobiomes Journal ◽

10.1094/pbiomes-11-18-0055-r ◽

2019 ◽

Vol 3 (3) ◽

pp. 212-223 ◽

Cited By ~ 3

Author(s):

Yuan Zeng ◽

Zaid Abdo ◽

Amy Charkowski ◽

Jane E. Stewart ◽

Kenneth Frost

Keyword(s):

Community Structure ◽

Microbial Communities ◽

Management Practices ◽

Soil Microbial Communities ◽

Alpha Diversity ◽

Potato Production ◽

Crop Species ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Sample Depth

1,3-Dichloropropene (1,3-D) is a well-known nematicidal soil fumigant on many crop species. Currently, little is known about its impact on soil microbial communities using culture-free methods. In this study, we investigated changes in soil bacterial and fungal diversity and composition at two depths (30.5 and 61 cm) in response to management practices of applying 1,3-D at four different rates (103, 122, 140, and 187 liters/ha) relative to an untreated control in potato production fields using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. A total of 12,783 operational taxonomic units (OTUs) for 16S and 1,706 OTUs for ITS were obtained. Sequencing revealed that Proteobacteria, Firmicutes, Actinobacteria, and Ascomycota were dominant phyla in soils. Comparing alpha diversity of microbial communities at the different chemical rates with untreated plots showed that bacterial communities in plots treated with 1,3-D fumigation at 140 liters/ha were richer, which was supported by higher richness indices. Other diversity indices and overall soil microbial community structure were not significantly influenced by any rates of 1,3-D fumigation, although higher bacterial and fungal richness and diversity were observed in posttreatment soils and/or at 30.5 cm. Of the identified microbial families, the differential abundance of 45 bacterial and 24 fungal families was affected by sample depth, 1,3-D rate, or the interaction of sample depth and 1,3-D. The bacterial family Enterobacteriaceae, which includes species that specialize in decay of complex carbohydrates, increased in abundance post-1,3-D fumigation, and the fungal family Ophiocordycipitaceae, which includes nematode and insect pathogens, decreased, suggesting that the nematode and soil insect death caused by fumigation may selectively impact specific fungal and bacterial families.

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Response of soil microbial communities to different management practices in surface soils of a soybean agroecosystem in Argentina

European Journal of Soil Biology ◽

10.1016/j.ejsobi.2010.11.006 ◽

2011 ◽

Vol 47 (1) ◽

pp. 55-60 ◽

Cited By ~ 52

Author(s):

S. Vargas Gil ◽

J. Meriles ◽

C. Conforto ◽

M. Basanta ◽

V. Radl ◽

...

Keyword(s):

Microbial Communities ◽

Management Practices ◽

Soil Microbial Communities ◽

Surface Soils ◽

Soil Microbial

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Changes in composition and activity of soil microbial communities in peach and kiwifruit Mediterranean orchards under an innovative management system

Soil Research ◽

10.1071/sr09128 ◽

2010 ◽

Vol 48 (3) ◽

pp. 266 ◽

Cited By ~ 7

Author(s):

Adriano Sofo ◽

Giuseppe Celano ◽

Patrizia Ricciuti ◽

Maddalena Curci ◽

Bartolomeo Dichio ◽

...

Keyword(s):

Microbial Communities ◽

Cover Crops ◽

Denaturing Gradient Gel Electrophoresis ◽

Diversity Index ◽

Soil Depth ◽

Soil Microbial Communities ◽

Soil Management ◽

Organic Input ◽

Soil Microbial ◽

Peach Orchard

The aim of this work was to evaluate the effects of 2 soil management systems, so called ‘innovative’ (INN) and ‘conventional’ (CON), on genetic and metabolic diversity of soil microbial communities of peach and kiwifruit orchards. INN system included minimum tillage, organic matter inputs from compost and cover crops, winter pruning, and adequate irrigation and fertilisation. CON system was characterised by conventional tillage, zero organic input, empirical pruning, strong chemical fertilisation, and excessive irrigation. After 4 years of treatments, soil samples were collected in different orchard sites. In peach and kiwifruit INN orchards, average fruit yields were significantly higher than in CON. INN orchards had a significantly higher total number of bacteria. The patterns of denaturing gradient gel electrophoresis of bacterial 16S rDNA/RNA from peach orchard showed differences between soils under drip emitters and along the inter-rows, whereas those from kiwifruit orchard clearly distinguished between INN and CON for both bacteria (16S rRNA) and fungi (18S rDNA/RNA). Shannon’s substrate diversity index, evaluated by Biolog® metabolic assay, was affected by soil treatment in peach orchard and by soil depth in kiwifruit orchard. Principal component analysis of Biolog® values clearly discriminated INN and CON soils of both orchards. The results revealed qualitative and quantitative changes of soil microbial communities in response to an innovative and sustainable soil management.

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Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil

Applied and Environmental Microbiology ◽

10.1128/aem.02278-19 ◽

2019 ◽

Vol 86 (5) ◽

Cited By ~ 2

Author(s):

Yang Ouyang ◽

Jeanette M. Norton

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Enzyme Activities ◽

Bacterial Communities ◽

N Mineralization ◽

Management Practices ◽

Soil Microbial Communities ◽

N Fertilization ◽

Soil Microbial ◽

N Management

ABSTRACT Soil extracellular enzymes play a significant role in the N mineralization process. However, few studies have documented the linkage between enzyme activity and the microbial community that performs the function. This study examined the effects of inorganic and organic N fertilization on soil microbial communities and their N mineralization functions over 4 years. Soils were collected from silage corn field plots with four contrasting N treatments: control (no additional N), ammonium sulfate (AS; 100 and 200 kg of N ha−1), and compost (200 kg of N ha−1). Illumina amplicon sequencing was used to comprehensively assess the overall bacterial community (16S rRNA genes), bacterial ureolytic community (ureC), and bacterial chitinolytic community (chiA). Selected genes involved in N mineralization were also examined using quantitative real-time PCR and metagenomics. Enzymes (and marker genes) included protease (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF). Compost significantly increased diversity of overall bacterial communities even after one application, while ammonium fertilizers had no influence on the overall bacterial communities over four seasons. Bacterial ureolytic and chitinolytic communities were significantly changed by N fertilization. Compost treatment strongly elevated soil enzyme activities after 4 years of repeated application. Functional gene abundances were not significantly affected by N treatments, and they were not correlated with corresponding enzyme activities. N mineralization genes were recovered from soil metagenomes based on a gene-targeted assembly. Understanding how the structure and function of soil microbial communities involved with N mineralization change in response to fertilization practices may indicate suitable agricultural management practices that improve ecosystem services while reducing negative environmental consequences. IMPORTANCE Agricultural N management practices influence the enzymatic activities involved in N mineralization. However, specific enzyme activities do not identify the microbial species directly involved in the measured process, leaving the link between the composition of the microbial community and the production of key enzymes poorly understood. In this study, the application of high-throughput sequencing, real-time PCR, and metagenomics shed light on how the abundance and diversity of microorganisms involved in N mineralization respond to N management. We suggest that N fertilization has significantly changed bacterial ureolytic and chitinolytic communities.

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