Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments.

Applied Microbiology and Biotechnology
Dongwei HouZhijian Huang

Abstract

Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond ...Continue Reading

References

Apr 28, 2001·Journal of Experimental Marine Biology and Ecology·Y -C. Lin, J -C. Chen
Jan 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·Noah Fierer, Robert B Jackson
May 30, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jizhong ZhouCharles T Garten
Mar 6, 2009·Bioresource Technology·Qunlan ZhouLiu Bo
Aug 14, 2009·Ecology Letters·Noah FiererCory C Cleveland
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Aug 14, 2010·Proceedings of the National Academy of Sciences of the United States of America·Irina Dana OfiteruWilliam T Sloan
Aug 17, 2010·Bioinformatics·Robert C Edgar
Dec 21, 2010·Ecology Letters·Hélène MorlonJessica L Green
Mar 5, 2011·Microbiology and Molecular Biology Reviews : MMBR·Ryan J NewtonStefan Bertilsson
Apr 22, 2011·Environmental Microbiology·Robert I GriffithsAndrew S Whiteley
Apr 27, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jennifer B H MartinyM Claire Horner-Devine
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
May 15, 2012·Nature Reviews. Microbiology·China A HansonJennifer B H Martiny
Jun 7, 2013·The ISME Journal·James C StegenAllan Konopka
Feb 20, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jizhong ZhouAdam P Arkin
Jun 4, 2014·The ISME Journal·Peter De Schryver, Olav Vadstein
Dec 15, 2015·International Journal of Food Microbiology·D Sylvain DabadéHeidy M W den Besten
Feb 24, 2016·Frontiers in Microbiology·Loh Teng-Hern TanBey-Hing Goh
Oct 13, 2017·Microbiology and Molecular Biology Reviews : MMBR·Jizhong Zhou, Daliang Ning
Nov 29, 2017·Antonie van Leeuwenhoek·Jing ZhangZong-Jun Du
Jan 20, 2018·Science·Manuel Delgado-BaquerizoNoah Fierer
Jul 25, 2019·Nature Medicine·Clea BárcenaCarlos López-Otín
Aug 14, 2020·Nature Reviews. Microbiology·Pankaj TrivediBrajesh K Singh
Feb 6, 2021·Applied Microbiology and Biotechnology·Zhongyi LuMeng Li

❮ Previous
Next ❯

Citations

Oct 9, 2021·Environmental Science and Pollution Research International·Xiuli ChenShuguang Xie

❮ Previous
Next ❯

Software Mentioned

R
BioEnv
QIIME
vegan
ANOSIM
UCLUST

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.