Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life

Abdallah, Rehab Z.; Wegner, Carl‐Eric; Liesack, Werner

doi:10.1016/j.soilbio.2019.01.023

Cited by 30 publications

(16 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genes for GHs (EC 3.2.1.‐) are involved in catalysing the hydrolysis of glycosidic bond of glycosides. Together with PLs and CEs, these enzymes were often related to organic C decomposition and the AAs were related to lignin decomposition (Abdallah et al ., 2019). By contrast, the genes for GTs (EC 2.4.‐.‐) involved in catalysing the formation of the glycosidic bond to form a glycoside, related to organic C biosynthesis (Pold et al ., 2016).…”

Section: Methodsmentioning

confidence: 99%

Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences

Dai

Zang

Chen

et al. 2021

Environmental Microbiology

View full text Add to dashboard Cite

Summary Diversity and community composition of soil microorganisms along the elevation climosequences have been widely studied, while the microbial metabolic potential, particularly in regard to carbon (C) cycling, remains unclear. Here, a metagenomic analysis of C related genes along five elevations ranging from 767 to 4190 m at Mount Kilimanjaro was analysed to evaluate the microbial organic C transformation capacities in various ecosystems. The highest gene abundances for decomposition of moderate mineralizable compounds, i.e. carbohydrate esters, chitin and pectin were found at the mid‐elevations with hump‐shaped pattern, where the genes for decompositions of recalcitrant C (i.e. lignin) and easily mineralizable C (i.e. starch) showed the opposite trend (i.e. U‐shaped pattern), due to high soil pH and seasonality in both low and high elevations. Notably, the gene abundances for the decompositions of starch, carbohydrate esters, chitin and lignin had positive relationships with corresponding C compounds, indicating the consistent responses of microbial functional profiles and metabolites to elevation climosequences. Understanding of adaptation of microbial communities, potential function and metabolites to elevation climosequences and their influencing factors provided a new insight for the regulation of terrestrial C storage.

show abstract

Section: Methodsmentioning

confidence: 99%

Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences

Dai

Zang

Chen

et al. 2021

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…The feeding preferences of the biocontrol agent are one of the major determinants in developing specific rhizosphere microbiome (Gao et al 2019 ). The interactions between different trophic levels (an organism’s position it occupies in a food web) can modify the nutrient cycling and influence soil nutrient status and plant nutrition (Abdallah et al 2019 ) that further affects the soil suppressiveness (Krištůfek et al 2000 ).…”

Section: Biotic Contributors To Disease-suppressive Soilsmentioning

confidence: 99%

Disease-Suppressive Soils—Beyond Food Production: a Critical Review

Somasundaram

Naorem

Lal

et al. 2021

J Soil Sci Plant Nutr

View full text Add to dashboard Cite

In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.

show abstract

“…(3) Production of CH 4 in flooded soils requires the presence of a sufficient number of the microbes involved. Even more importantly, it is necessary that the microbes are not only present but express sufficient activity [ 55 , 56 , 57 , 58 ]. (4) The microorganisms involved in CH 4 production are more or less sensitive to O 2 .…”

Section: Observations In Accordance With Theorymentioning

confidence: 99%

Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation

Conrad

2020

Microorganisms

View full text Add to dashboard Cite

Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O2. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH4. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O2 to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH4 production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH4, probably due to the peculiarities of the resident methanotrophic bacteria.

show abstract

Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life

Cited by 30 publications

References 82 publications

Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences

Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences

Disease-Suppressive Soils—Beyond Food Production: a Critical Review

Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation

Contact Info

Product

Resources

About