Deciphering bacterial interactions via DSF-regulated public goods in an anammox community

2019 ◽  
Author(s):  
Yongzhao Guo ◽  
Yunpeng Zhao ◽  
Xi Tang ◽  
Tianxing Na ◽  
Juejun Pan ◽  
...  
Keyword(s):  
Amino Acids ◽  
Microbial Community ◽  
Public Goods ◽  
Extracellular Polymeric Substances ◽  
Microbial Interactions ◽  
Anammox Bacteria ◽  
Signal Molecules ◽  
Bacteria Growth ◽  
Bacterial Interactions ◽  
Social Traits

Abstract Background: Bacterial interaction and communication via quorum sensing (QS) received extensively attention, as it can coordinate bacterial behavior and activity through the QS signal molecules in microbial community. Though the exchange of public goods regulated by QS have been explored in pure culture, how signal sense, transmit, and affect the social traits through regulating public goods in complex communities remains unclear. Results: The levels of public goods (e.g. extracellular polymeric substances (EPS) and amino acids) changed significantly when exogenous diffusion signal factor (DSF), a kind of QS molecules, was added. Approaches involving meta-omics and hierarchical signalling network construction give insight into that anammox species ( Jettenia caeni , AMX1) and Proteobacteria -affiliated bacterium (PRO1) can sense and transit DSF signals, thus directly regulating the production and exchange of public goods via the secondary messenger c-di-GMP regulator, Clp. In detail, these two kinds of species can supply more costly amino acids for DSF-Secretor species (like AMX2, CFX1, CFX3, and PRO4) after sensing DSF. Meanwhile, DSF-Secretor species encoded diverse genes involved in hydrolysis of extracellular protein and carbohydrate and genes involved in transportation of peptides and sugars. The exogenous DSF-inducement also leads to the high expression of these genes, which indicated DSF-Secretor species helped anammox bacteria scavenge extracellular detritus. This process can be considered as a feedback of public goods supply by anammox bacteria, as this process contributed to create a suitable environment for anammox bacteria growth. Namely, DSF can bridge bacterial interactions through regulating public goods. Furthermore, the trade-off induces discrepant metabolic loads of different microbial clusters and community succession. It illustrated the potential to artificially alleviate metabolic loads and thus increase proliferation rate for certain bacteria through QS. Conclusions: DSF can bridge interactions of anammox bacteria and DSF-Secretor species through regulating production and exchange of public goods using Clp regulator. Deciphering microbial interactions via QS provides insights for understanding the molecular evolution of QS in microbial community.

scholarly journals Response and Adaptation of Microbial Community in a CANON Reactor Exposed to an Extreme Alkaline Shock

Archaea ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Ruili Yang ◽  
Wenlong Mao ◽  
Xiaojun Wang ◽  
Zhaoji Zhang ◽  
Junbin Wu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Influencing Factors ◽  
Relative Abundance ◽  
Nitrogen Removal ◽  
Extracellular Polymeric Substances ◽  
Recovery Phase ◽  
Nitrogen Loading ◽  
Anammox Bacteria ◽  
Anammox Activity ◽  
Canon Process

Responses of a microbial community in the completely autotrophic nitrogen removal over nitrite (CANON) process, which was shocked by a pH of 11.0 for 12 h, were investigated. During the recovery phase, the performance, anaerobic ammonia oxidation (anammox) activity, microbial community, and correlation of bacteria as well as the influencing factors were evaluated synchronously. The performance of the CANON process deteriorated rapidly with a nitrogen removal rate (NRR) of 0.13 kg·m-3·d-1, and Firmicutes, spore-forming bacteria, were the dominant phyla after alkaline shock. However, it could self-restore within 107 days after undergoing four stages, at which Planctomycetes became dominant with a relative abundance of 64.62%. Network analysis showed that anammox bacteria (Candidatus Jettenia, Kuenenia, and Brocadia) were positively related to some functional bacteria such as Nitrosomonas, SM1A02, and Calorithrix. Canonical correspondence analysis presented a strong correlation between the microbial community and influencing factors during the recovery phase. With the increase of nitrogen loading rate, the decrease of free nitrous acid and the synergistic effects, heme c content, specific anammox activity (SAA), NRR, and the abundance of dominant genus increased correspondingly. The increase of heme c content regulates the quorum sensing system, promotes the secretion of extracellular polymeric substances, and further improves SAA, NRR, and the relative abundance of the dominant genus. This study highlights some implications for the recovery of the CANON reactor after being exposed to an alkaline shock.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

Deciphering bacterial social traits via diffusible signal factor (DSF) -mediated public goods in an anammox community

2021 ◽  
pp. 116802
Author(s):  
Yongzhao Guo ◽  
Yunpeng Zhao ◽  
Xi Tang ◽  
Tianxing Na ◽  
Juejun Pan ◽  
...  
Keyword(s):  
Public Goods ◽  
Social Traits ◽  
Diffusible Signal Factor

scholarly journals Positive linkage between bacterial social traits reveals that homogeneous rather than specialized behavioral repertoires prevail in natural Pseudomonas communities

2018 ◽  
Author(s):  
Jos Kramer ◽  
Miguel Ángel López Carrasco ◽  
Rolf Kümmerli
Keyword(s):  
Public Goods ◽  
Bacterial Communities ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Social Strategies ◽  
Toxic Compounds ◽  
Social Traits ◽  
Social Type ◽  
Social Trait ◽  
Limited Scope

ABSTRACTBacteria frequently cooperate by sharing secreted metabolites such as enzymes and siderophores. The expression of different ‘public good’ traits can be interdependent, and studies on laboratory systems have shown that such trait linkage affects eco-evolutionary dynamics within bacterial communities. Here, we examine whether linkage among social traits occurs in natural Pseudomonas communities by examining investment levels and correlations between five public goods: biosurfactants, biofilm components, proteases, pyoverdines, and toxic compounds. Our phenotypic assays involving 315 isolates from soil and freshwater communities revealed that their social trait expression profiles varied dramatically, and that correlations between traits were frequent, exclusively positive, and sometimes habitat-specific. Our results indicate that Pseudomonas communities are dominated by isolates lying on a continuum between a ‘social’ type producing multiple public goods, and an ‘asocial’ type showing low investment into social traits. This segregation into different social types could reflect local adaptation to different microhabitats, or emerge from competition between different (social) strategies. Moreover, our results show that isolates with specialized trait repertoires are rare, suggesting limited scope for the mutual exchange of different public goods between isolates. Overall, our work indicates that complex interdependencies among social traits influence the evolution of microbial lifestyles in nature.

scholarly journals Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

2020 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Chrissy Sherrill ◽  
Matthew A Davis ◽  
Kylie Kavanagh
Keyword(s):  
Microbial Community ◽  
Systemic Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Vervet Monkeys ◽  
Fecal Samples ◽  
Age Related ◽  
Rrna Gene Sequencing ◽  
The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

scholarly journals Achieving fast start-up of anammox process by promoting the growth of anammox bacteria with FeS addition

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Chunzhen Zou ◽  
Beibei Guo ◽  
Xuming Zhuang ◽  
Liying Ren ◽  
Shou-Qing Ni ◽  
...  
Keyword(s):  
Microbial Community ◽  
Nitrogen Removal ◽  
Nitrite Reductase ◽  
Removal Rate ◽  
Anammox Bacteria ◽  
Gene Encoding ◽  
Start Up ◽  
Fast Start ◽  
The Difference ◽  
Anammox Process

Abstract The effects of FeS on nitrogen removal performance and microbial community of anammox process were studied. During the start-up period, the removal efficiencies of nitrite and total nitrogen were significantly improved by FeS. The addition of FeS increased the content of iron ions in the reactor and promoted the synthesis of heme c, which was involved in the formation of various enzymes. Compared with the control, the abundance of anammox bacteria in the FeS reactor was increased by 29%, and the expression level of the nirS gene (encoding cd1 type nitrite reductase containing heme) was nearly doubled. The content of nitrite reductase (ammonia-forming) in the community was increased by 26.4%. The difference in functional bacteria and enzyme contents in the microbial community resulted in a difference in nitrogen removal rate (NRR) between the two reactors. High-throughput results indicated that FeS increased the richness and diversity of microbial community and enhanced the metabolic function of the microbial community. The addition of FeS did not change the dominant position of Ca. Kuenenia in both reactors. But the relative abundance of heterotrophic denitrifying bacteria was reduced with FeS, which may be related to the inhibition effect of S2− produced by FeS.

scholarly journals Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates

2020 ◽  
Vol 8 (3) ◽  
pp. 314
Author(s):  
Qianqian Li ◽  
Rebecca E. Cooper ◽  
Carl-Eric Wegner ◽  
Kirsten Küsel
Keyword(s):  
Hot Spots ◽  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Molecular Mechanisms ◽  
Core Genome ◽  
Gene Clusters ◽  
Microbial Interactions ◽  
Aggregate Formation ◽  
Rna Seq ◽  
Metabolic Potential

Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/− 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.

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