scholarly journals Metabarcoding Reveals Lacustrine Picocyanobacteria Respond to Environmental Change Through Adaptive Community Structuring

2021 ◽  
Vol 12 ◽  
Author(s):  
Lena A. Schallenberg ◽  
John K. Pearman ◽  
Carolyn W. Burns ◽  
Susanna A. Wood
Keyword(s):  
Environmental Change ◽  
Environmental Variables ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Epifluorescence Microscopy ◽  
Environmental Drivers ◽  
Rrna Gene ◽  
Community Adaptation ◽  
Phylogenetic Studies ◽  
Community Data

Picocyanobacteria (Pcy) are important yet understudied components of lake foodwebs. While phylogenetic studies of isolated strains reveal a high diversity of freshwater genotypes, little is known about abiotic drivers associated with Pcy in different lakes. Due to methodological limitations, most previous studies assess potential drivers using total cell abundances as a response, with often conflicting and inconsistent results. In the present study, we explored how picocyanobacterial communities respond to environmental change using a combination of epifluorescence microscopy and community data determined using 16S rRNA gene metabarcoding. Temporal shifts in picocyanobacterial abundance, diversity and community dynamics were assessed in relation to potential environmental drivers in five contrasting lakes over 1year. Cell abundances alone were not consistently related to environmental variables across lakes. However, the addition of metabarcoding data revealed diverse picocyanobacterial communities that differed significantly between lakes, driven by environmental variables related to trophic state. Within each lake, communities were temporally dynamic and certain amplicon sequence variants (ASVs) were strongly associated with specific environmental drivers. Rapid shifts in community structure and composition were often related to environmental changes, indicating that lacustrine Pcy can persist at high abundances through collective community adaptation. These results demonstrate that a combination of microscopy and metabarcoding enables an in-depth characterisation of picocyanobacterial communities and reveals strain-specific drivers. We recommend that future studies cease referring to picocyanobacterial as one functional group and take strain specific variability into consideration.

scholarly journals DNA from lake sediments reveals the long-term dynamics and diversity of <i>Synechococcus</i> assemblages

2013 ◽  
Vol 10 (6) ◽  
pp. 3817-3838 ◽  
Author(s):  
I. Domaizon ◽  
O. Savichtcheva ◽  
D. Debroas ◽  
F. Arnaud ◽  
C. Villar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Environmental Conditions ◽  
Trophic Status ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Quantitative Polymerase Chain Reaction ◽  
Additive Models ◽  
Phosphorus Concentration ◽  
Rrna Gene

Abstract. While picocyanobacteria (PC) are important actors in carbon and nutrient cycles in aquatic systems, factors controlling their interannual dynamics and diversity are poorly known due to the general lack of long-term monitoring surveys. This study intended to fill this gap by applying a DNA-based paleolimnological approach to sediment records from a deep subalpine lake that has experienced dramatic changes in environmental conditions during the last century (eutrophication, re-oligotrophication and large-scale climate changes). In particular, we investigated the long-term (100 yr) diversity and dynamics of Synechococcus,, PC that have presumably been affected by both the lake trophic status changes and global warming. The lake's morphological and environmental conditions provided the ideal conditions for DNA preservation in the sediment archives. Generalised additive models applied to quantitative PCR (qPCR; quantitative Polymerase Chain Reaction) results highlighted that an increase in summer temperature could have a significant positive impact on the relative abundance of Synechococcus, (fraction of Synechococcus, in total cyanobacteria). The diversity of Synechococcus, in Lake Bourget was studied by phylogenetic analyses of the 16S rRNA gene and the following internally transcribed spacer (ITS). Up to 23 different OTUs (based on 16S rRNA), which fell into various cosmopolitan or endemic clusters, were identified in samples from the past 100 yr. Moreover, the study of ITS revealed a higher diversity within the major 16S rRNA-defined OTUs. Changes in PC diversity were related to the lake's trophic status. Overall, qPCR and sequencing results showed that environmental changes (in temperature and phosphorus concentration) affected Synechococcus, community dynamics and structure, translating into changes in genotype composition. These results also helped to re-evaluate the geographical distribution of some Synechococcus, clusters. Providing such novel insights into the long-term history of an important group of primary producers, this study illustrates the promising approach that consists in coupling molecular tools and paleolimnology to reconstruct a lake's biodiversity history.

scholarly journals Urbanization-induced environmental changes strongly affect wetland soil bacterial community composition and diversity

2021 ◽  
Author(s):  
Xinyu Yi ◽  
Chen Ning ◽  
Shuailong Feng ◽  
Haiqiang Gao ◽  
Jianlun Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Drivers ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Soil Microbial ◽  
Soil Bacterial

Abstract Soil microbial communities potentially serve as indicators for their responses to changes in various ecosystems at scales from a region to the globe. However, changes in wetland soil bacterial communities and how they are related to urbanization intensities remains poorly understood. Here, we collected sixty soil samples along urbanization intensity gradients from twenty wetlands. We measured a range of environmental factors and characterized bacterial communities structure using 16S rRNA gene amplicon sequencing that targeted the V4-V5 region. Our results revealed the dominant soil microbial phyla included Proteobacteria (39.3%), Acidobacteria (21.4%) and Chloroflexi (12.3%) in the wetlands, and showed a significant divergence of composition in intensive urbanization area (UI_4) than other places. A critical "threshold" exists in the soil bacterial diversity, demonstrating different patterns: a gradual increase in the areas of low-to-intermediate disturbances but a significant decrease in highly urbanized areas where metabolic functions were significantly strong. Additionally, soil pH, total phosphorus (TP), available phosphorus (AP ) and ammonia nitrogen (NH4+-N) made a significant contribution to variations in bacterial communities, explaining 49.6%, 35.1%, 26.2% and 30.7% of the total variance, respectively. pH and NH4+-N were identified as the main environmental drivers to determine bacterial community structure and diversity in the urban wetlands. Our results highlight collective changes in multiple environmental variables induced by urbanization rather than by the proportion of impervious surface area (ISA), which were potentially attributed to the spatial heterogeneity along different urbanization gradients.

scholarly journals Biological and environmental drivers of deep-sea benthic ecosystem functioning in Canada’s Laurentian Channel Area of Interest (AOI)

2018 ◽  
Author(s):  
Marta Miatta ◽  
Paul V Snelgrove
Keyword(s):  
Deep Sea ◽  
Ecosystem Functioning ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Environmental Drivers ◽  
Biological Traits ◽  
Area Of Interest ◽  
Prokaryotic Abundance

Ongoing environmental changes and accelerating biodiversity loss raise concern and interest about the role of environmental factors and biodiversity in determining marine ecosystem functioning. This study aims to identify the main drivers of benthic ecosystem functioning in deep-sea sedimentary habitats in the Laurentian Channel Area of Interest (AOI), and in particular the role of sea pens (Pennatulacea) as potential keystone species in the area. Using the ROV ROPOS we collected sediment cores and measured environmental variables from 6 stations inside the AOI (depths 348–445m) in September 2017. Through 48-hours incubations and flux measurements (oxygen, inorganic nutrients), we estimated organic matter remineralization, a key benthic function. Preliminary analyses show no significant variation in fluxes among stations, despite significant differences in environmental variables However, the presence/absence of Pennatulacea inside the cores indicated some capability to enhance remineralization and particularly nitrification. Ongoing analyses will address sediment properties, macrofaunal biodiversity, prokaryotic abundance, and biological traits as drivers of remineralization. Shedding new light on the primary drivers of ecosystem functioning in the area will inform the design or monitoring strategies proposed for this AOI and offer new perspectives and tools for MPA design.

scholarly journals Biological and environmental drivers of deep-sea benthic ecosystem functioning in Canada’s Laurentian Channel Area of Interest (AOI)

2018 ◽  
Author(s):  
Marta Miatta ◽  
Paul V Snelgrove
Keyword(s):  
Deep Sea ◽  
Ecosystem Functioning ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Environmental Drivers ◽  
Biological Traits ◽  
Area Of Interest ◽  
Prokaryotic Abundance

Ongoing environmental changes and accelerating biodiversity loss raise concern and interest about the role of environmental factors and biodiversity in determining marine ecosystem functioning. This study aims to identify the main drivers of benthic ecosystem functioning in deep-sea sedimentary habitats in the Laurentian Channel Area of Interest (AOI), and in particular the role of sea pens (Pennatulacea) as potential keystone species in the area. Using the ROV ROPOS we collected sediment cores and measured environmental variables from 6 stations inside the AOI (depths 348–445m) in September 2017. Through 48-hours incubations and flux measurements (oxygen, inorganic nutrients), we estimated organic matter remineralization, a key benthic function. Preliminary analyses show no significant variation in fluxes among stations, despite significant differences in environmental variables However, the presence/absence of Pennatulacea inside the cores indicated some capability to enhance remineralization and particularly nitrification. Ongoing analyses will address sediment properties, macrofaunal biodiversity, prokaryotic abundance, and biological traits as drivers of remineralization. Shedding new light on the primary drivers of ecosystem functioning in the area will inform the design or monitoring strategies proposed for this AOI and offer new perspectives and tools for MPA design.

scholarly journals Fine-Scale Mapping of Mega-Epibenthic Communities and Their Patch Characteristics on Two New Zealand Seamounts

2021 ◽  
Vol 8 ◽  
Author(s):  
Savannah L. Goode ◽  
Ashley A. Rowden ◽  
David A. Bowden ◽  
Malcolm R. Clark ◽  
Fabrice Stephenson
Keyword(s):  
Community Structure ◽  
New Zealand ◽  
Environmental Variables ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Benthic Communities ◽  
Environmental Drivers ◽  
Fine Scale ◽  
Patch Characteristics ◽  
Epibenthic Communities

Seamounts are common features of the deep seafloor that are often associated with aggregations of mega-epibenthic fauna, including deep-sea corals and sponges. Globally, many seamounts also host abundant fish stocks, supporting commercial bottom trawl fisheries that impact non-target benthic species through damage and/or removal of these non-target species. However, the effects of bottom trawling on seamount benthic communities, as well as their recovery potential, will vary over the total seamount area because of differences in within seamount habitat and community structure. It is therefore important to understand fine-scale community dynamics, community patch characteristics, and the environmental drivers contributing to these patterns to improve habitat mapping efforts on seamounts and to determine the potential for benthic communities on seamounts to recover from fishing disturbances. Here we analysed the structure and distribution of mega-epibenthic communities on two New Zealand seamounts with different physical environments to determine which environmental variables best correlated with variation in community structure within each seamount. We used the identified environmental variables to predict the distribution of communities beyond the sampled areas, then described the spatial patterns and patch characteristics of the predicted community distributions. We found the environmental variables that best explained variations in community structure differed between the seamounts and at different spatial scales. These differences were reflected in the distribution models: communities on one seamount were predicted to form bands with depth, while on the other seamount communities varied mostly with broadscale aspect and the presence of small pinnacles. The number and size of community patches, inter-patch distances, and patch connectedness were found to differ both within and between seamounts. These types of analyses and results can be used to inform the spatial management of seamount ecosystems.

scholarly journals Machine Learning Predicts the Presence of 2,4,6-Trinitrotoluene in Sediments of a Baltic Sea Munitions Dumpsite Using Microbial Community Compositions

2021 ◽  
Vol 12 ◽  
Author(s):  
René Janßen ◽  
Aaron J. Beck ◽  
Johannes Werner ◽  
Olaf Dellwig ◽  
Johannes Alneberg ◽  
...  
Keyword(s):  
Machine Learning ◽  
Microbial Community ◽  
Baltic Sea ◽  
Microbial Communities ◽  
Environmental Variables ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
R Package ◽  
Environmental Drivers ◽  
Rrna Gene

Bacteria are ubiquitous and live in complex microbial communities. Due to differences in physiological properties and niche preferences among community members, microbial communities respond in specific ways to environmental drivers, potentially resulting in distinct microbial fingerprints for a given environmental state. As proof of the principle, our goal was to assess the opportunities and limitations of machine learning to detect microbial fingerprints indicating the presence of the munition compound 2,4,6-trinitrotoluene (TNT) in southwestern Baltic Sea sediments. Over 40 environmental variables including grain size distribution, elemental composition, and concentration of munition compounds (mostly at pmol⋅g–1 levels) from 150 sediments collected at the near-to-shore munition dumpsite Kolberger Heide by the German city of Kiel were combined with 16S rRNA gene amplicon sequencing libraries. Prediction was achieved using Random Forests (RFs); the robustness of predictions was validated using Artificial Neural Networks (ANN). To facilitate machine learning with microbiome data we developed the R package phyloseq2ML. Using the most classification-relevant 25 bacterial genera exclusively, potentially representing a TNT-indicative fingerprint, TNT was predicted correctly with up to 81.5% balanced accuracy. False positive classifications indicated that this approach also has the potential to identify samples where the original TNT contamination was no longer detectable. The fact that TNT presence was not among the main drivers of the microbial community composition demonstrates the sensitivity of the approach. Moreover, environmental variables resulted in poorer prediction rates than using microbial fingerprints. Our results suggest that microbial communities can predict even minor influencing factors in complex environments, demonstrating the potential of this approach for the discovery of contamination events over an integrated period of time. Proven for a distinct environment future studies should assess the ability of this approach for environmental monitoring in general.

scholarly journals DNA from lake sediments reveals the long-term dynamics and diversity of <i>Synechococcus</i> assemblages

2013 ◽  
Vol 10 (2) ◽  
pp. 2515-2564 ◽  
Author(s):  
I. Domaizon ◽  
O. Savichtcheva ◽  
D. Debroas ◽  
F. Arnaud ◽  
C. Villar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Environmental Conditions ◽  
Trophic Status ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Positive Impact ◽  
Additive Models ◽  
Phosphorus Concentration ◽  
Rrna Gene

Abstract. While picocyanobacteria (PC) are important actors in carbon and nutrient cycles in aquatic systems, factors controlling their interannual dynamics and diversity are poorly known due to the general lack of long-term monitoring surveys. This study intended to fill this gap by applying a DNA-based paleolimnological approach to sediment records from a deep subalpine lake that has experienced dramatic changes in environmental conditions during the last century (eutrophication, re-oligotrophication and large-scale climate changes). We particularly investigated the long-term (100 yr) diversity and dynamics of Synechococcus, PC that have presumably been affected by both the lake trophic status changes and global warming. The lake's morphological and environmental conditions provided ideal conditions for DNA preservation in the sediment archives. Generalised additive models applied to quantitative PCR (qPCR) results highlighted that an increase in summer temperature could have a significant positive impact on the relative abundance of Synechococcus (fraction of Synechococcus in total cyanobacteria). The diversity of Synechococcus in Lake Bourget was studied by phylogenetic analyses of the 16S rRNA gene and internal transcribed spacer (ITS). Up to 23 different OTUs (based on 16S rRNA), which fell into various cosmopolitan or endemic clusters, were identified in samples from the past 100 yr. Moreover, study of the ITS revealed a higher diversity within the major 16S rRNA-defined OTUs. Changes in PC diversity were related to the lake's trophic status. Overall, qPCR and sequencing results showed that environmental changes (here, in temperature and phosphorus concentration) affected Synechococcus community dynamics and structure, translating into changes in genotype composition. These results also helped to re-evaluate the geographical distribution of some Synechococcus clusters. Providing such novel insights into the long-term history of an important group of primary producers, this study illustrates the promising approach that consists in coupling molecular tools and paleolimnology to reconstruct a lake's biodiversity history.

scholarly journals Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 27
Author(s):  
Hyo-Ryeon Kim ◽  
Jae-Hyun Lim ◽  
Ju-Hyoung Kim ◽  
Il-Nam Kim
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Marine Bacteria ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Composition Data ◽  
Decomposition Of Organic Matter ◽  
Class Level ◽  
Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

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