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

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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Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes

Microorganisms ◽

10.3390/microorganisms10010140 ◽

2022 ◽

Vol 10 (1) ◽

pp. 140

Author(s):

Wenjing Liu ◽

Kai Xue ◽

Runpeng Hu ◽

Jizhong Zhou ◽

Joy D. Van Nostrand ◽

...

Keyword(s):

Microbial Communities ◽

Gene Diversity ◽

Soil Microbial Communities ◽

Short Rotation Coppice ◽

Functional Genes ◽

Long Term Effects ◽

Soil Microbial ◽

Biogeographic Pattern ◽

Short Rotation

Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3−-N and P concentrations. The microbial taxa–area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m2, which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term.

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Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition

npj Biofilms and Microbiomes ◽

10.1038/s41522-021-00187-7 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Ying Gao ◽

Junjun Ding ◽

Mengting Yuan ◽

Nona Chiariello ◽

Kathryn Docherty ◽

...

Keyword(s):

Microbial Community ◽

Soil Microbial Communities ◽

Taxonomic Composition ◽

Functional Gene ◽

Functional Genes ◽

Detectable Effect ◽

Soil Microbial ◽

Soil Variables ◽

Soil Bacterial

AbstractClimate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.

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Long-term Application of Manure Alters Culturable Soil Microbial Populations and Leads to Occurrence of Antibiotic resistant Bacteria

Soil and Sediment Contamination An International Journal ◽

10.1080/15320383.2021.1961122 ◽

2021 ◽

pp. 1-15

Author(s):

Yalda Mahjoory ◽

Nasser Aliasgharzad ◽

Gholamali Moghaddam ◽

Ahmad Bybordi

Keyword(s):

Microbial Populations ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant ◽

Soil Microbial

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Comparing the long-term responses of soil microbial structures and diversities to polyethylene microplastics in different aggregate fractions

Environment International ◽

10.1016/j.envint.2021.106398 ◽

2021 ◽

Vol 149 ◽

pp. 106398

Author(s):

Junhua Hou ◽

Xiangjian Xu ◽

Hong Yu ◽

Beidou Xi ◽

Wenbing Tan

Keyword(s):

Soil Microbial ◽

Microbial Structures ◽

Aggregate Fractions

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Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems

Agriculture ◽

10.3390/agriculture11050445 ◽

2021 ◽

Vol 11 (5) ◽

pp. 445

Author(s):

Jessica Cuartero ◽

Onurcan Özbolat ◽

Virginia Sánchez-Navarro ◽

Marcos Egea-Cortines ◽

Raúl Zornoza ◽

...

Keyword(s):

Microbial Community ◽

Crop Yield ◽

Soil Microbial Community ◽

Cropping Systems ◽

Sequencing Analysis ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Network Analyses ◽

Organic Cultivation

Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.

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