Stressor interactions under differential exogenous microbial exposure in Daphnia magna_revised

Stressor interactions under differential exogenous microbial exposure in Daphnia magna_version2

10.31219/osf.io/mske8 ◽

2021 ◽

Author(s):

Shira Houwenhuyse ◽

Lore Bulteel ◽

Naina Goel ◽

Isabel Vanoverberghe ◽

Ellen Decaestecker

Keyword(s):

Body Size ◽

Microbial Community ◽

Microbial Communities ◽

Stress Responses ◽

Multiple Stressors ◽

Natural Environments ◽

Laboratory Setting ◽

Natural Conditions ◽

Aspergillus Aculeatus ◽

Diverse Microbial Community

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.

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Stressor interactions under differential exogenous microbial exposure in Daphnia magna

10.31219/osf.io/3vgdh ◽

2021 ◽

Author(s):

Shira Houwenhuyse ◽

Lore Bulteel ◽

Naina Goel ◽

Isabel Vanoverberghe ◽

Ellen Decaestecker

Keyword(s):

Body Size ◽

Microbial Communities ◽

Daphnia Magna ◽

Stress Responses ◽

Multiple Stressors ◽

Natural Environments ◽

Laboratory Setting ◽

Natural Conditions ◽

Aspergillus Aculeatus ◽

Diverse Microbial Community

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.

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Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

10.21203/rs.3.rs-33130/v1 ◽

2020 ◽

Author(s):

Oskar Modin ◽

Raquel Liebana ◽

Soroush Saheb-Alam ◽

Britt-Marie Wilén ◽

Carolina Suarez ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Null Model ◽

Amplicon Sequencing ◽

Null Models ◽

Marker Genes ◽

Experimental Systems ◽

Microbial Community Assembly ◽

The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Molecules ◽

10.3390/molecules26237332 ◽

2021 ◽

Vol 26 (23) ◽

pp. 7332

Author(s):

Miguel David Marfil-Santana ◽

Anahí Martínez-Cárdenas ◽

Analuisa Ruíz-Hernández ◽

Mario Vidal-Torres ◽

Norma Angélica Márquez-Velázquez ◽

...

Keyword(s):

Microbial Community ◽

Secondary Metabolites ◽

Microbial Communities ◽

Secondary Metabolite ◽

Resistant Bacteria ◽

Mangrove Sediments ◽

Molecular Networking ◽

Mangrove Tree ◽

Enhanced Production ◽

The Impact

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

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Spatiotemporal Correlations Between Water Quality And Microbial Community of Typical Inflow River Into Taihu Lake, China

10.21203/rs.3.rs-1000115/v1 ◽

2021 ◽

Author(s):

Yajie Zhang ◽

Ye Zhang ◽

Lecheng Wei ◽

Mengyan Li ◽

Weitang Zhu ◽

...

Keyword(s):

Water Quality ◽

Microbial Community ◽

Microbial Communities ◽

Taihu Lake ◽

Wastewater Treatment Plants ◽

Ammonia Nitrogen ◽

Pollution Sources ◽

Storm Water ◽

Urban Wastewater Treatment ◽

The Impact

Abstract Changxing River, which is a typical inflow river into the Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, storm water outlets, and non-point source agricultural drainage areas are chosen, and next-generation sequencing and multi-variate statistical analyses are used to characterize the microbial communities and reveal their relationship with water physicochemical properties. Results showed that ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) are the main pollutant in Changxing River, especially at storm water outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant phyla included Proteobacteria (40.9%), Bacteroidetes (21.0%) and Euryarchaeota (6.1%) under the condition of algal bloom. Water temperature (T), air pressure (P), concentrations of TP and CODMn were the important variables for the succession of microbial community. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO3--N) at storm water outlets. The results provide a reference for the impact of pollution types on river microbial ecosystem under complex hydrological condition and a guidance for the selection of restoration techniques for polluted rivers entering an important lake.

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Impact of Soil Drying-Rewetting Stress on Microbial Communities and Activities and on Degradation of Two Crop Protection Products

Applied and Environmental Microbiology ◽

10.1128/aem.70.5.2577-2587.2004 ◽

2004 ◽

Vol 70 (5) ◽

pp. 2577-2587 ◽

Cited By ~ 96

Author(s):

Manuel Pesaro ◽

Gilles Nicollier ◽

Josef Zeyer ◽

Franco Widmer

Keyword(s):

16S Rrna ◽

Microbial Communities ◽

Stress Responses ◽

Crop Protection ◽

16S Rrna Genes ◽

Cell Counting ◽

Rrna Genes ◽

Soil Dna ◽

Degradation Rates ◽

The Impact

ABSTRACT Prior to registration of crop protection products (CPPs) their persistence in soil has to be determined under defined conditions. For this purpose, soils are collected in the field and stored for up to 3 months prior to the tests. During storage, stresses like drying may induce changes in microbiological soil characteristics (MSCs) and thus may influence CPP degradation rates. We investigated the influence of soil storage-related stress on the resistance and resilience of different MSCs by assessing the impact of a single severe drying-rewetting cycle and by monitoring recovery from this event for 34 days. The degradation and mineralization of the fungicide metalaxyl-M and the insecticide lufenuron were delayed by factors of 1.5 to 5.4 in the dried and rewetted soil compared to the degradation and mineralization in an undisturbed reference. The microbial biomass, as estimated by direct cell counting and from the soil DNA content, decreased on average by 51 and 24%, respectively. The bulk microbial activities, as determined by measuring substrate-induced respiration and fluorescein diacetate hydrolysis, increased after rewetting and recovered completely within 6 days after reequilibration. The effects on Bacteria, Archaea, and Pseudomonas were investigated by performing PCR amplification of 16S rRNA genes and reverse-transcribed 16S rRNA, followed by restriction fragment length polymorphism (RFLP) and terminal RFLP (T-RFLP) fingerprinting. Statistical analyses of RFLP and T-RFLP profiles indicated that specific groups in the microbial community were sensitive to the stress. In addition, evaluation of rRNA genes and rRNA as markers for monitoring the stress responses of microbial communities revealed overall similar sensitivities. We concluded that various structural and functional MSCs were not resistant to drying-rewetting stress and that resilience depended strongly on the parameter investigated.

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Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community

The ISME Journal ◽

10.1038/s41396-020-00755-3 ◽

2020 ◽

Vol 14 (11) ◽

pp. 2877-2889 ◽

Cited By ~ 1

Author(s):

Daniel Padfield ◽

Alex Vujakovic ◽

Steve Paterson ◽

Rob Griffiths ◽

Angus Buckling ◽

...

Keyword(s):

Microbial Community ◽

Focal Species ◽

Natural Microbial Community ◽

The Impact

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Erosion reduces soil microbial diversity, network complexity and multifunctionality

The ISME Journal ◽

10.1038/s41396-021-00913-1 ◽

2021 ◽

Author(s):

Liping Qiu ◽

Qian Zhang ◽

Hansong Zhu ◽

Peter B. Reich ◽

Samiran Banerjee ◽

...

Keyword(s):

Soil Erosion ◽

Microbial Diversity ◽

Microbial Communities ◽

Negative Impact ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Relative Abundances ◽

The Impact

AbstractWhile soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

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Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.665090 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shengqiao Long ◽

Hui Tong ◽

Xuxiang Zhang ◽

Shuyu Jia ◽

Manjia Chen ◽

...

Keyword(s):

Heavy Metal ◽

Microbial Community ◽

Microbial Communities ◽

Southern China ◽

Risk Index ◽

River Sediments ◽

Microbial Community Composition ◽

Heavy Metal Tolerance ◽

Waste Recycling ◽

The Impact

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

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Costly learning: preference for familiar food persists despite negative impact on survival

Biology Letters ◽

10.1098/rsbl.2016.0256 ◽

2016 ◽

Vol 12 (7) ◽

pp. 20160256 ◽

Cited By ~ 4

Author(s):

Thaiany M. Costa ◽

Eileen A. Hebets ◽

Diogo Melo ◽

Rodrigo H. Willemart

Keyword(s):

Decision Making ◽

Food Choice ◽

Negative Impact ◽

Food Preferences ◽

Learning Preference ◽

Dog Food ◽

Experience Based Learning ◽

Impact On Survival ◽

Learned Preference ◽

The Impact

Animals often rely on events in their environment that provide information (i.e. experience) to alter their future decision-making in ways that are presumed to be beneficial. Such experience-based learning, however, does not always lead to adaptive decision-making. In this study, we use the omnivorous harvestman Heteromitobates discolor to explore the role of past diet on subsequent food choice and survival. We first tested whether a short-term homogeneous diet (rotten crickets, fresh crickets or dog food) influenced subsequent food choice (rotten cricket versus fresh cricket). We next examine the impact of diet on survival. We found that following experience with a homogeneous cricket diet, adult harvestmen displayed a learned preference for familiar food, regardless of whether it was rotten or fresh crickets; individuals experiencing dog food were equally likely to choose rotten versus fresh crickets. We additionally found that individuals that ate rotten crickets suffered shorter survival than those that ate fresh crickets. Together, our results suggest that the diet an individual experiences can lead to maladaptive food preferences—preferences that ultimately result in reduced longevity.

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