RNA-seq provides molecular insights into interaction modification in simplified microbial community

A major challenge in microbial ecology is to understand the stability of interspecies interactions when progressing from pairs of interacting species to multispecies interaction networks. A lack of direct evidence, and a conceptual framework to explore how direct and indirect effects shape cellular responses in species-rich networks has hindered progress in our understanding of these combined effects. Here we aimed to investigate whether higher-order interactions shape community dynamics and transcriptional profiles of all interacting partners in a simplified microbial community that includes a primary producer (Nannochloropsis oceanica CCAP849/10) and two heterotrophic bacteria (Marinobacter sp. FDB33 and Alteromonas sp. FDB36). By combining co-cultivation assays, quantification of absolute abundances, nutrient analysis, and simultaneous RNA-sequencing, we reveal genome-wide transcriptional responses in all binary co-cultivation partners and show that the third partner can profoundly alter binary interactions at the phenotypic and transcription level. Our study demonstrates the context-dependency of binary interactions, whereby environmental conditions and the presence of specific organisms can affect the cellular physiology of the interacting partners and ultimately the stability of the community. Furthermore, our approach provides a powerful tool for probing the molecular basis of emergent properties in more complex systems.

Download Full-text

Microbial dynamics in a High-Arctic glacier forefield: a combined field, laboratory, and modelling approach

10.5194/bg-2016-52 ◽

2016 ◽

Author(s):

James A. Bradley ◽

Sandra Arndt ◽

Marie Šabacká ◽

Liane G. Benning ◽

Gary L. Barker ◽

...

Keyword(s):

Microbial Community ◽

Numerical Model ◽

Microbial Communities ◽

Community Dynamics ◽

Heterotrophic Bacteria ◽

High Arctic ◽

Soil Development ◽

Arctic Soils ◽

Field Laboratory ◽

Modelling Approach

Abstract. Modelling the development of soils in glacier forefields is necessary in order to assess how microbial and geochemical processes interact and shape soil development in response to glacier retreat. Furthermore, such models can help us predict microbial growth and the fate of Arctic soils in an increasingly ice-free future. Here, for the first time, we combined field sampling with laboratory analyses and numerical modelling to investigate microbial community dynamics in oligotrophic proglacial soils in Svalbard. We measured low bacterial growth rates and growth efficiencies (relative to estimates from Alpine glacier forefields), and high sensitivity to soil temperature (relative to temperate soils). We used these laboratory measurements to inform parameter values in a new numerical model and significantly refined predictions of microbial and biogeochemical dynamics of soil development over a period of roughly 120 years. The model predicted the observed accumulation of autotrophic and heterotrophic biomass. Genomic data indicated that initial microbial communities were dominated by bacteria derived from the subglacial environment, whereas older soils hosted a mixed community of autotrophic and heterotrophic bacteria. This finding was validated by the numerical model, which showed that active microbial communities play key roles in fixing and recycling carbon and nutrients. We also demonstrated the role of allochthonous carbon and microbial necromass in sustaining a pool of organic material, despite high heterotrophic activity in older soils. This combined field, laboratory and modelling approach demonstrates the value of integrated model-data studies to understand and quantify the functioning of the microbial community in an emerging High-Arctic soil ecosystem.

Download Full-text

StreptomycesVolatile Compounds Influence Exploration and Microbial Community Dynamics by Altering Iron Availability

mBio ◽

10.1128/mbio.00171-19 ◽

2019 ◽

Vol 10 (2) ◽

Cited By ~ 9

Author(s):

Stephanie E. Jones ◽

Christine A. Pham ◽

Matthew P. Zambri ◽

Joseph McKillip ◽

Erin E. Carlson ◽

...

Keyword(s):

Microbial Community ◽

Nutrient Availability ◽

Iron Uptake ◽

Community Dynamics ◽

Critical Role ◽

Iron Availability ◽

Interspecies Interactions ◽

Community Interactions ◽

Content Type ◽

Bacteria And Fungi

ABSTRACTBacteria and fungi produce a wide array of volatile organic compounds (VOCs), and these can act as chemical cues or as competitive tools. Recent work has shown that the VOC trimethylamine (TMA) can promote a new form ofStreptomycesgrowth, termed “exploration.” Here, we report that TMA also serves to alter nutrient availability in the area surrounding exploring cultures: TMA dramatically increases the environmental pH and, in doing so, reduces iron availability. This, in turn, compromises the growth of other soil bacteria and fungi. In response to this low-iron environment,Streptomyces venezuelaesecretes a suite of differentially modified siderophores and upregulates genes associated with siderophore uptake. Further reducing iron levels by limiting siderophore uptake or growing cultures in the presence of iron chelators enhanced exploration. Exploration was also increased whenS. venezuelaewas grown in association with the related low-iron- and TMA-tolerantAmycolatopsisbacteria, due to competition for available iron. We are only beginning to appreciate the role of VOCs in natural communities. This work reveals a new role for VOCs in modulating iron levels in the environment and implies a critical role for VOCs in modulating the behavior of microbes and the makeup of their communities. It further adds a new dimension to our understanding of the interspecies interactions that influenceStreptomycesexploration and highlights the importance of iron in exploration modulation.IMPORTANCEMicrobial growth and community interactions are influenced by a multitude of factors. A new mode ofStreptomycesgrowth—exploration—is promoted by interactions with the yeastSaccharomycescerevisiaeand requires the emission of trimethylamine (TMA), a pH-raising volatile compound. We show here that TMA emission also profoundly alters the environment around exploring cultures. It specifically reduces iron availability, and this in turn adversely affects the viability of surrounding microbes. Paradoxically,Streptomycesbacteria thrive in these iron-depleted niches, both rewiring their gene expression and metabolism to facilitate iron uptake and increasing their exploration rate. Growth in close proximity to other microbes adept at iron uptake also enhances exploration. Collectively, the data from this work reveal a new role for bacterial volatile compounds in modulating nutrient availability and microbial community behavior. The results further expand the repertoire of interspecies interactions and nutrient cues that impactStreptomycesexploration and provide new mechanistic insight into this unique mode of bacterial growth.

Download Full-text

All-In-One: Microbial Response to Natural and Anthropogenic Forcings in a Coastal Mediterranean Ecosystem, the Syracuse Bay (Ionian Sea, Italy)

Journal of Marine Science and Engineering ◽

10.3390/jmse10010019 ◽

2021 ◽

Vol 10 (1) ◽

pp. 19

Author(s):

Gabriella Caruso ◽

Maria Grazia Giacobbe ◽

Filippo Azzaro ◽

Franco Decembrini ◽

Marcella Leonardi ◽

...

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Community Dynamics ◽

Heterotrophic Bacteria ◽

Nutrient Concentrations ◽

Mediterranean Ecosystem ◽

Organic Substrates ◽

Metabolic Potential ◽

Microbial Response ◽

Phytoplankton Communities

Bacterial and phytoplankton communities are known to be in close relationships, but how natural and anthropogenic stressors can affect their dynamics is not fully understood. To study the response of microbial communities to environmental and human-induced perturbations, phytoplankton and bacterial communities were seasonally monitored in a Mediterranean coastal ecosystem, Syracuse Bay, where multiple conflicts co-exist. Quali-quantitative, seasonal surveys of the phytoplankton communities (diatoms, dinoflagellates and other taxa), the potential microbial enzymatic activity rates (leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) and heterotrophic culturable bacterial abundance, together with the thermohaline structure and trophic status in terms of nutrient concentrations, phytoplankton biomass (as Chlorophyll-a), and total suspended and particulate organic matter, were carried out. The aim was to integrate microbial community dynamics in the context of the environmental characterization and disentangle microbial patterns related to natural changes from those driven by the anthropic impact on this ecosystem. In spite of the complex relationships between the habitat characteristics, microbial community abundance and metabolic potential, in Syracuse Bay, the availability of organic substrates differently originated by the local conditions appeared to drive the distribution and activity of microbial assemblage. A seasonal pattern of microbial abundances was observed, with the highest concentrations of phytoplankton in spring and low values in winter, whereas heterotrophic bacteria were more abundant during the autumn period. The autumn peaks of the rates of enzymatic activities suggested that not only phytoplankton-derived but also allochthonous organic polymers strongly stimulated microbial metabolism. Increased microbial response in terms of abundance and metabolic activities was detected especially at the sites directly affected by organic matter inputs related to agriculture or aquaculture activities. Nitrogen salts such as nitrate, rather than orthophosphate, were primary drivers of phytoplankton growth. This study also provides insights on the different seasonal scenarios of water quality in Syracuse Bay, which could be helpful for management plans of this Mediterranean coastal environment.

Download Full-text

Interspecies interactions are an integral determinant of microbial community dynamics

Frontiers in Microbiology ◽

10.3389/fmicb.2015.01148 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 7

Author(s):

Fatma A. A. Aziz ◽

Kenshi Suzuki ◽

Akihiro Ohtaki ◽

Keita Sagegami ◽

Hidetaka Hirai ◽

...

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Interspecies Interactions ◽

Microbial Community Dynamics

Download Full-text

High resolution single cell analytics to follow microbial community dynamics in anaerobic ecosystems

Methods ◽

10.1016/j.ymeth.2012.04.001 ◽

2012 ◽

Vol 57 (3) ◽

pp. 338-349 ◽

Cited By ~ 18

Author(s):

Susann Müller ◽

Thomas Hübschmann ◽

Sabine Kleinsteuber ◽

Carsten Vogt

Keyword(s):

Microbial Community ◽

High Resolution ◽

Single Cell ◽

Community Dynamics ◽

Microbial Community Dynamics ◽

Resolution Single

Download Full-text

Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

Waste Management ◽

10.1016/j.wasman.2015.05.012 ◽

2015 ◽

Vol 43 ◽

pp. 114-122 ◽

Cited By ~ 39

Author(s):

Qigui Niu ◽

Yasuyuki Takemura ◽

Kengo Kubota ◽

Yu-You Li

Keyword(s):

Microbial Community ◽

Anaerobic Digestion ◽

Community Dynamics ◽

Chicken Manure ◽

Microbial Community Dynamics ◽

Thermophilic Anaerobic Digestion

Download Full-text

Responses of simultaneous anammox and denitrification (SAD) process to nitrogen loading variation: Start-up, performance, sludge morphology and microbial community dynamics

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.148911 ◽

2021 ◽

pp. 148911

Author(s):

Shun Zhou ◽

Zhi Zhang ◽

Zhulong Sun ◽

Zhuangzhuang Song ◽

Yun Bai ◽

...

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Nitrogen Loading ◽

Microbial Community Dynamics ◽

Start Up

Download Full-text

Root influence on soil nitrogen availability and microbial community dynamics results in contrasting rhizosphere priming effects in pine and spruce soil

Functional Ecology ◽

10.1111/1365-2435.13797 ◽

2021 ◽

Author(s):

Jian Li ◽

Saeed Alaei ◽

Moyan Zhou ◽

Per Bengtson

Keyword(s):

Microbial Community ◽

Soil Nitrogen ◽

Nitrogen Availability ◽

Community Dynamics ◽

Soil Nitrogen Availability ◽

Priming Effects ◽

Microbial Community Dynamics

Download Full-text

Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

Journal of Food Protection ◽

10.4315/0362-028x-68.1.40 ◽

2005 ◽

Vol 68 (1) ◽

pp. 40-48 ◽

Cited By ~ 40

Author(s):

ANABELLE MATOS ◽

JAY L. GARLAND

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Dynamics ◽

Community Level ◽

Microbial Consortia ◽

Single Strain ◽

Acridine Orange Staining ◽

Physiological Profiles ◽

Alfalfa Sprouts ◽

Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

Download Full-text