Exploring the interaction patterns in seasonal marine microbial communities with network analysis

2013 ◽  
Author(s):  
Shao-Wu Zhang ◽  
Ze-Gang Wei ◽  
Chen Zhou ◽  
Yu-Chen Zhang ◽  
Ting-He Zhang
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
Interaction Patterns ◽  
Marine Microbial Communities

Enhanced CO2 concentrations change the structure of Antarctic marine microbial communities

2016 ◽  
Vol 552 ◽  
pp. 93-113 ◽  
Author(s):  
AT Davidson ◽  
J McKinlay ◽  
K Westwood ◽  
PG Thomson ◽  
R van den Enden ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Co2 Concentrations ◽  
Antarctic Marine ◽  
Marine Microbial Communities

scholarly journals Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Yoshitake ◽  
Gaku Kimura ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Pacific Coast ◽  
Three Dimensional ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Shotgun Metagenomics ◽  
Functional Features ◽  
Pacific Coast Of Japan ◽  
Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

scholarly journals Future Climate Alters Pathogens-Microbiome Co-occurrence Networks in Wheat Straw Residues during Decomposition

Proceedings ◽  
2021 ◽  
Vol 66 (1) ◽  
pp. 22
Author(s):  
Sara Fareed Mohamed Wahdan ◽  
François Buscot ◽  
Witoon Purahong
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
Wheat Straw ◽  
Pathogenic Fungi ◽  
Future Climate ◽  
Plant Residues ◽  
Plant Pathogenic Fungi ◽  
Plant Growth Promoting Bacteria ◽  
Ambient Conditions ◽  
Ecological Functions

The return of plant residues to the ground is used to promote soil carbon sequestration, improve soil structure, reduce evaporation, and help to fix additional carbon dioxide in the soil. The microbial communities with diverse ecological functions that colonize plant residues during decomposition are expected to be highly dynamic. We aimed to characterize microbial communities colonizing wheat straw residues and their ecological functions during the early phase of straw decomposition. The experiment, run in Central Germany, was conducted in a conventional farming system under both ambient conditions and a future climate scenario expected in 50–70 years from now. We used MiSeq illumina sequencing and network analysis of bacterial 16S rRNA and fungal ITS genes. Our results show that future climate alters the dynamics of bacterial and fungal communities during decomposition. We detected various microbial ecological functions within wheat straw residues such as plant growth-promoting bacteria, N-fixing bacteria, saprotrophs, and plant pathogenic fungi. Interestingly, plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome under both ambient and future climate conditions. Therefore, we applied co-occurrence network analysis to predict the potential impacts of climate change on the interaction between pathogenic community and other bacterial and fungal microbiomes. The network under ambient climate consisted of 91 nodes and 129 correlations (edges). The highest numbers of connections were detected for the pathogens Mycosphaerella tassiana and Neosetophoma rosigena. The network under future climate consisted of 100 nodes and 170 correlations. The highest numbers of connections were detected for the pathogens Pseudopithomyces rosae and Gibellulopsis piscis. We conclude that the future climate significantly changes the interactions between plant pathogenic fungi and other microorganisms during the early phrase of decomposition.

scholarly journals Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

2022 ◽  
Author(s):  
Gayathri Sambamoorthy ◽  
Karthik Raman
Keyword(s):  
Microbial Communities ◽  
In Silico ◽  
Microbial Interactions ◽  
Interaction Patterns ◽  
Wild Type ◽  
Community Function ◽  
Evolutionary Forces ◽  
In Silico Studies ◽  
Wide Range ◽  
In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

scholarly journals The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0142690 ◽  
Author(s):  
Zilian Zhang ◽  
Yi Chen ◽  
Rui Wang ◽  
Ruanhong Cai ◽  
Yingnan Fu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Exopolysaccharide ◽  
Marine Microbial Communities

New Technologies, New Horizons

2011 ◽  
pp. 23-41
Author(s):  
Hiller A. Spires ◽  
Meixun Zheng ◽  
Manning Pruden
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Graduate Students ◽  
Network Analysis ◽  
New Technologies ◽  
Interaction Patterns ◽  
Teaching With Technology ◽  
Graduate Course ◽  
Pedagogical Content ◽  
New Horizons

The purpose of this chapter is to present graduate students’ views of their Technological Pedagogical Content Knowledge (TPACK) development. These graduate students are also teachers. Data was collected using a mixed method approach founded on the TPACK Framework and social network analysis. Koehler and Mishra (2006) claim that effective teaching with technology requires TPACK, or an ability to integrate content, pedagogy and technology flexibly during the act of teaching. As part of a graduate course on new literacies and media, participants were required to design and implement lessons that incorporated a range of technologies, produce written reflections about their experiences, and engage in online interactions with participants in the class. Qualitative results from participants’ written reflections revealed four themes relative to TPACK. Additionally, a social network analysis demonstrated a positive relationship between participants’ views on their TPACK development and their interaction patterns within the online learning environment. This study shows that the TPACK framework can be a useful tool, giving educators a productive way to think about technology integration as they navigate the rapid changes prompted by emerging technologies.

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