scholarly journals Stressor interactions under differential exogenous microbial exposure in Daphnia magna_version2

2021 ◽  
Author(s):  
Shira Houwenhuyse ◽  
Lore Bulteel ◽  
Naina Goel ◽  
Isabel Vanoverberghe ◽  
Ellen Decaestecker

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory setting often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated how stressor responses differed between laboratory and natural conditions in Daphnia magna when exposed to single or multiple stressors. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows that natural environments have a more diverse microbial community compared with laboratory conditions, which was ultimately reflected in the gut microbiomes after inoculation. Stressor responses in Daphnia were affected by their bacterial environment for survival, but not for fecundity and body size. Fecuntiy and body size did show a main stressor effect, which could possibly be linked with stessor-specific microbiomes (for Microcystis and the combined stressor treatment). In addition, genotype-specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.

2021 ◽  
Author(s):  
Shira Houwenhuyse ◽  
Lore Bulteel ◽  
Naina Goel ◽  
Isabel Vanoverberghe ◽  
Ellen Decaestecker

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory setting often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated how stressor responses differed between laboratory and natural conditions in Daphnia magna when exposed to single or multiple stressors. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows that natural environments have a more diverse microbial community compared with laboratory conditions, which was ultimately reflected in the gut microbiomes after inoculation. Stressor responses in Daphnia were affected by their bacterial environment for survival, but not for fecundity and body size. Fecuntiy and body size did show a main stressor effect, which could possibly be linked with stessor-specific microbiomes (for Microcystis and the combined stressor treatment). In addition, genotype-specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.


2021 ◽  
Author(s):  
Shira Houwenhuyse ◽  
Lore Bulteel ◽  
Naina Goel ◽  
Isabel Vanoverberghe ◽  
Ellen Decaestecker

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory settings often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated the impact of single versus simultaneous multiple stressor exposure on Daphnia magna life history traits and whether this tolerance was microbiome-mediated. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows survival in Daphnia was microbiome-mediated as survival was only negatively impacted when Daphnia received a lab microbial community. Daphnia which received a natural microbial community have a broader environmental pool of microbiota to randomnly and selectively take up and showed no negative impact on survival. Simultaneous exposure to both stressors also revealed an antagonistic interaction for survival. Fecundity and body size were negatively impacted by exposure to stress, however, responses were here not microbiome-mediated. In addition, genotype specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.


2019 ◽  
Author(s):  
Xiaochu Li ◽  
Floricel Gonzalez ◽  
Nathaniel Esteves ◽  
Birgit E. Scharf ◽  
Jing Chen

AbstractCoexistence of bacteriophages, or phages, and their host bacteria plays an important role in maintaining the microbial communities. In natural environments with limited nutrients, motile bacteria can actively migrate towards locations of richer resources. Although phages are not motile themselves, they can infect motile bacterial hosts and spread in space via the hosts. Therefore, in a migrating microbial community coexistence of bacteria and phages implies their co-propagation in space. Here, we combine an experimental approach and mathematical modeling to explore how phages and their motile host bacteria coexist and co-propagate. When lytic phages encountered motile host bacteria in our experimental set up, a sector-shaped lysis zone formed. Our mathematical model indicates that local nutrient depletion and the resulting inhibition of proliferation and motility of bacteria and phages are the key to formation of the observed lysis pattern. The model further reveals the straight radial boundaries in the lysis pattern as a tell-tale sign for coexistence and co-propagation of bacteria and phages. Emergence of such a pattern, albeit insensitive to extrinsic factors, requires a balance between intrinsic biological properties of phages and bacteria, which likely results from co-evolution of phages and bacteria.Author summaryCoexistence of phages and their bacterial hosts is important for maintaining the microbial communities. In a migrating microbial community, coexistence between phages and host bacteria implies that they co-propagate in space. Here we report a novel phage lysis pattern that is indicative of this co-propagation. The corresponding mathematical model we developed highlights a crucial dependence of the lysis pattern and implied phage-bacteria co-propagation on intrinsic properties allowing proliferation and spreading of the microbes in space. Remarkably, extrinsic factors, such as overall nutrient level, do not influence phage-bacteria coexistence and co-propagation. Findings from this work have strong implications for dispersal of phages mediated by motile bacterial communities, which will provide scientific basis for the fast-growing applications of phages.


2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun

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.


2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.


2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.


Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.


Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2299
Author(s):  
Jéssica P. Silva ◽  
Alonso R. P. Ticona ◽  
Pedro R. V. Hamann ◽  
Betania F. Quirino ◽  
Eliane F. Noronha

Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zala Schmautz ◽  
Carlos A. Espinal ◽  
Andrea M. Bohny ◽  
Fabio Rezzonico ◽  
Ranka Junge ◽  
...  

Abstract Background An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. Results We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. Conclusion Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.


2020 ◽  
Vol 401 (12) ◽  
pp. 1365-1374
Author(s):  
Daniel K.H. Rode ◽  
Praveen K. Singh ◽  
Knut Drescher

AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.


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