scholarly journals Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces

2021 ◽  
Vol 12 ◽  
Author(s):  
Marino Korlević ◽  
Marsej Markovski ◽  
Zihao Zhao ◽  
Gerhard J. Herndl ◽  
Mirjana Najdek
Keyword(s):  
Microbial Communities ◽  
Seasonal Dynamics ◽  
Microbial Community Composition ◽  
Growth Cycle ◽  
High Rank ◽  
Ambient Water ◽  
Phylogenetic Groups ◽  
Marine Macrophytes ◽  
Macrophyte Growth ◽  
Epiphytic Communities

Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.

scholarly journals Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments

2020 ◽  
Author(s):  
Júlia B. Gontijo ◽  
Andressa M. Venturini ◽  
Caio A. Yoshiura ◽  
Clovis D. Borges ◽  
José Mauro S. Moura ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Seasonal Dynamics ◽  
Abiotic Factors ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Chemistry ◽  
Floodplain Forests ◽  
Variable Environment ◽  
Floodplain Sediments

AbstractThe Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here we provide the first report of the in situ seasonal dynamics of CH4 cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH4 cycling microbial communities and further investigated their responses to seasonal changes. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the methanogenic (methyl coenzyme-M reductase – mcrA) and methanotrophic (particulate methane monooxygenase – pmoA) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry, but also the composition of the microbial communities. The results presented may contribute to the understanding of the current state of CH4 cycling in this region.

Structure and Seasonal Dynamics of Hyporheic Zone Microbial Communities in Free-Stone Rivers of the Western United States

2003 ◽  
Vol 46 (2) ◽  
pp. 200-215 ◽  
Author(s):  
K. P. Feris ◽  
P. W. Ramsey ◽  
C. Frazar ◽  
M. C. Rillig ◽  
J. E. Gannon ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Seasonal Dynamics ◽  
Hyporheic Zone ◽  
Western United States

scholarly journals Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

2015 ◽  
Vol 12 (13) ◽  
pp. 10359-10387 ◽  
Author(s):  
W. Y. Dong ◽  
X. Y. Zhang ◽  
X. Y. Liu ◽  
X. L. Fu ◽  
F. S. Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Chinese Fir ◽  
Subtropical China ◽  
Nitrogen And Phosphorus ◽  
Soil Microbial ◽  
Nutrient Additions

Abstract. Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation.

scholarly journals Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Vapor Flow ◽  
Arid Soils ◽  
Opposite Pattern ◽  
Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

scholarly journals Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms

2021 ◽  
Vol 9 (7) ◽  
pp. 1495
Author(s):  
Tim Piel ◽  
Giovanni Sandrini ◽  
Gerard Muyzer ◽  
Corina P. D. Brussaard ◽  
Pieter C. Slot ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Glycoside Hydrolases ◽  
Microbial Community Analysis ◽  
Cyanobacterial Blooms ◽  
Temporary Increase ◽  
Low Concentrations ◽  
Harmful Cyanobacterial Blooms

Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

scholarly journals Temporal and spatial dynamics of peat microbiomes in drained and rewetted soils of three temperate peatlands

2020 ◽  
Author(s):  
Haitao Wang ◽  
Micha Weil ◽  
Dominik Zak ◽  
Diana Münch ◽  
Anke Günther ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Community Composition ◽  
Structural Equation ◽  
Structural Equation Models ◽  
Temporal Dynamics ◽  
Salt Water ◽  
Microbial Community Composition ◽  
Gas Emissions

AbstractBackgroundDrainage of high-organic peatlands for agricultural purposes has led to increased greenhouse gas emissions and loss of biodiversity. In the last decades, rewetting of peatlands is on the rise worldwide, to mitigate these negative impacts. However, it remains still questionable how rewetting would influence peat microbiota as important drivers of nutrient cycles and ecosystem restoration. Here, we investigate the spatial and temporal dynamics of the diversity, community composition and network interactions of prokaryotes and eukaryotes, and the influence of rewetting on these microbial features in formerly long-term drained and agriculturally used fens. Peat-soils were sampled seasonally from three drained and three rewetted sites representing the dominating fen peatland types of glacial landscapes in Northern Germany, namely alder forest, costal fen and percolation fen.ResultsCostal fens as salt-water impacted systems showed a lower microbial diversity and their microbial community composition showed the strongest distinction from the other two peatland types. Prokaryotic and eukaryotic community compositions showed a congruent pattern which was mostly driven by peatland type and rewetting. Rewetting decreased the abundances of fungi and prokaryotic decomposers, while the abundance of potential methanogens was significantly higher in the rewetted sites. Rewetting also influenced the abundance of ecological clusters in the microbial communities identified from the co-occurrence network. The microbial communities changed only slightly with depth and over time. According to structural equation models rewetted conditions affected the microbial communities through different mechanisms across the three studied peatland types.ConclusionsOur results suggest that rewetting strongly impacts the structure of microbial communities and, thus, important biogeochemical processes, which may explain the high variation in greenhouse gas emissions upon rewetting of peatlands. The improved understanding of functional mechanisms of rewetting in different peatland types lays the foundation for securing best practices to fulfil multiple restoration goals including those targeting on climate, water, and species protection.

scholarly journals Selective DNA and Protein Isolation From Marine Macrophyte Surfaces

2021 ◽  
Vol 12 ◽  
Author(s):  
Marino Korlević ◽  
Marsej Markovski ◽  
Zihao Zhao ◽  
Gerhard J. Herndl ◽  
Mirjana Najdek
Keyword(s):  
16S Rrna ◽  
High Specificity ◽  
Complete Removal ◽  
16S Rrna Sequencing ◽  
Cymodocea Nodosa ◽  
Protein Isolation ◽  
Marine Macrophytes ◽  
Rrna Sequencing ◽  
Epiphytic Communities ◽  
Sampling Season

Studies of unculturable microbes often combine methods, such as 16S rRNA sequencing, metagenomics, and metaproteomics. To apply these techniques to the microbial community inhabiting the surfaces of marine macrophytes, it is advisable to perform a selective DNA and protein isolation prior to the analysis to avoid biases due to the host material being present in high quantities. Two protocols for DNA and protein isolation were adapted for selective extractions of DNA and proteins from epiphytic communities inhabiting the surfaces of two marine macrophytes, the seagrass Cymodocea nodosa and the macroalga Caulerpa cylindracea. Protocols showed an almost complete removal of the epiphytic community regardless of the sampling season, station, settlement, or host species. The obtained DNA was suitable for metagenomic and 16S rRNA sequencing, while isolated proteins could be identified by mass spectrometry. Low presence of host DNA and proteins in the samples indicated a high specificity of the protocols. The procedures are based on universally available laboratory chemicals making the protocols widely applicable. Taken together, the adapted protocols ensure an almost complete removal of the macrophyte epiphytic community. The procedures are selective for microbes inhabiting macrophyte surfaces and provide DNA and proteins applicable in 16S rRNA sequencing, metagenomics, and metaproteomics.

Effect of ambient water conditions on microbial communities on the artificially produced aggregates: Evidence from experiments using two different seawater cultures

2021 ◽  
Author(s):  
Markus Weinbauer ◽  
Chiaki Motegi ◽  
Christophe Migon ◽  
Xavier Mari
Keyword(s):  
Microbial Communities ◽  
Water Flow ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Ambient Water ◽  
Lagoon Water ◽  
Water Conditions ◽  
Flow Experiment ◽  
Water Treatments

<p>Microbial communities on marine aggregates could be influenced by ambient water conditions; however, empirical data are scarce. In this study, we used fingerprint analysis of PCR-amplified 16S rRNA gene fragment to examine how microbial communities on aggregates change in response to different conditions of ambient water. We conducted two experiments using seawater cultures from surface waters of the lagoon and the anthropogenically influenced bay of Nouméa, New Caledonia: a transplant experiment in which the artificially produced aggregates from one station was added to ultra-filtered seawater culture of another station, and a water-flow experiment in which the artificially produced aggregates placed in the ultra-filtered seawater culture with or without water-flow. In a transplant experiment, bacterial community composition (BCC) on the bay and lagoon water aggregates were significantly different (<em>p < 0.05</em>, ANOSIM) at the beginning of experiment. After 11 days of incubation, BCC on the lagoon water aggregates were significantly different (<em>p < 0.05</em>) from transplanted communities. Transplantation effect was also observed in the bay water treatments. In a water-flow experiment, BCC on the bay and lagoon water aggregates were significantly different (<em>p < 0.05</em>) at the beginning of the experiment. BCC on the lagoon and bay water aggregates with and without water-flow treatments were significantly different (<em>p </em>< 0.05) at the end of incubation, and effect of water-flow on BCC were observed in the bay and lagoon water treatments. Our experimental studies suggest that changes in ambient water conditions potentially influence microbial communities on aggregates in the Bay of Nouméa.</p>

Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Trophic Interactions ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Trophic Levels ◽  
Soil Matrix ◽  
Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 µm) usually are more stable than macroaggregates (> 250 µm) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 µm – 2mm) and microaggregates (50 – 250 µm). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

2020 ◽  
Author(s):  
xia ding ◽  
Xiaojue Peng ◽  
Zhichao Chen ◽  
Yingjie Li ◽  
Lihui Mao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Drought Stress ◽  
Microbial Communities ◽  
Community Assembly ◽  
Wild Rice ◽  
Microbial Community Composition ◽  
Α Diversity ◽  
Oryza Longistaminata ◽  
Network Properties ◽  
Microbiome Assembly

Abstract Background Drought is a global environmental stress that limits crop yields. Microbial communities control many biogeochemical processes, and a predictive understanding of how crop microbial communities assemble in response to drought stress is central to addressing the challenges caused by drought. Little is known about the microbiome assembly processes in rice-ecosystems, particularly with regard to their environmental adaptation. Wild rice may serve as a source of superior drought tolerance candidate for rice breeding. There is an urgent need to explore wild rice resistance mechanisms to drought stress. Here, we evaluated the effect of drought stress on the microbial community recruitment and assembly in the endosphere (leaf, stem, and root) and rhizosphere of Oryza longistaminata. Results Species replacement was the dominant process shaping microbial community composition under drought stress. O. longistaminata recruited the phyla Actinobacteria and Fusobacteria, the genus Streptomyces, and phototrophic prokaryotes to improve its fitness. The host exerted strong effects on microbiome assembly, and the responses of the microbial community structure to the drought environment showed above- and belowground patterns. Drought reduced taxonomic α-diversity and destabilized co-occurrence network properties in the leaves and stems, but not in the roots and rhizosphere. Drought promoted the restructuring and strengthening of belowground network links to more strongly interconnect network properties. The drought response of the microbiome was phylogenetically conserved. Stochastic (neutral) processes acted on microbial community reassembly in response to drought stress across all four compartments. Conclusions Our results provide new insight into the mechanisms through which drought alters microbial community assembly in drought-tolerant wild rice and reveal a potential strategy for manipulating plant microbiomes to improve crop fitness.

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