AUTHOR=Chen Chen , Han Hui , Xu Ting , Lv Yizhong , Hu Kelin , Li Xue Xian , Qiao Yuhui , Ding Guo-Chun , Li Ji 

TITLE=Comparison of the Total, Diazotrophic and Ammonia-Oxidizing Bacterial Communities Between Under Organic and Conventional Greenhouse Farming

JOURNAL=Frontiers in Microbiology

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.01861

DOI=10.3389/fmicb.2020.01861

ISSN=1664-302X

ABSTRACT=<p>Organic greenhouse farming is an innovative system that may maintain a high yield and healthy agroecosystem. There have been no rigorous studies on the comparison of total and nitrogen-cycling bacterial community in vegetable soils between organic and conventional farming management at large scale. A survey of bacterial community and nitrogen cycles from soils under organic and conventional greenhouse farming was performed at 30 sites, covering seven soil types with 4 to 18 years of organic farming history. Communities of the total, diazotrophs and ammonia-oxidizing bacteria were studied with high-throughput sequencing of the 16S <italic>rRNA</italic>, <italic>nifH</italic> and <italic>amoA</italic> genes, respectively. Organic greenhouse farming did not influence alpha diversities. Beta diversities among the total (26/30) and diazotrophic (17/19) bacteria differed between farming systems, but compositional differences in ammonia-oxidizing bacteria between the two farming systems were only detected at 6 sites. Despite the effects of farming system on most bacterial genera were varied across different sites, organic greenhouse farming persistently selected for a few genera, possibly for the biodegradation of organic carbon with high molecular weight (<italic>Hyphomicrobium, Rubinisphaera, Aciditerrimonas, Planifilum, Phaselicystis</italic>, and <italic>Ohtaekwangia</italic>), but against putative ammonia oxidizing (<italic>Nitrosospira, Nitrosopumilus</italic>) and diazotrophic (<italic>Bradyrhizobium</italic>) bacterial genera, as determined by 16S <italic>rRNA</italic> analysis. Diazotrophic bacteria affiliated with <italic>nifH</italic> cluster 1J were preferentially associated with organic greenhouse farming, in contrast to <italic>Paenibacillus borealis</italic>. In summary, this study provides insights into the complex effects of organic greenhouse farming on the total, diazotrophic and ammonia oxidizing bacterial communities across different environmental context.</p>