scholarly journals Active or not? What microbial assemblages say about pockmarks located at Estremadura Spur (NE Atlantic)

2018 ◽  
Author(s):  
Clara F Rodrigues ◽  
Vitor Magalhães ◽  
Marina Cunha
Keyword(s):  
Community Structure ◽  
Ecosystem Functioning ◽  
Critical Role ◽  
Environmental Parameters ◽  
Marine Ecosystems ◽  
Biogeochemical Cycles ◽  
Ne Atlantic ◽  
Abundance And Distribution ◽  
Generation Sequencing ◽  
Hydrocarbon Degraders

Bacteria are important components of marine ecosystems and play a critical role in the biogeochemical cycles. Although ubiquitous and abundant in marine ecosystems, little is known about their diversity and composition, which is usually affected by several environmental parameters. Due to their abundance and distribution, which includes shallow-water locations, the contribution of pockmarks to global methane and hydrocarbon release could be massive. Microbial assemblages associated with pockmarks are known to be different between active and inactive sites. In this study, the microbial assemblages associated with several pockmarks located at the outer shelf of the Estremadura Spur were revealed using a next-generation sequencing of the bacterial/archaeal 16S RRNA. The sampled stations show a similar community structure for the most abundant phyla. OTUs encompass 59 bacterial and three archaeal phyla. Within Bacteria, Proteobacteria with 62.6% was the dominant phylum followed by Actinobacteria (7.8%), Acidobacteria (7.7%), Bacteroidetes (4.5%) and Gemmatimonadetes (2.8%). These groups are known to dominate marine sediments and their diversity was comparable to other studies. The studied microbial assemblages also comprised several phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders emphasizing its importance for the ecosystem functioning.

scholarly journals Active or not? What microbial assemblages say about pockmarks located at Estremadura Spur (NE Atlantic)

2018 ◽  
Author(s):  
Clara F Rodrigues ◽  
Vitor Magalhães ◽  
Marina Cunha
Keyword(s):  
Community Structure ◽  
Ecosystem Functioning ◽  
Critical Role ◽  
Environmental Parameters ◽  
Marine Ecosystems ◽  
Biogeochemical Cycles ◽  
Ne Atlantic ◽  
Abundance And Distribution ◽  
Generation Sequencing ◽  
Hydrocarbon Degraders

Bacteria are important components of marine ecosystems and play a critical role in the biogeochemical cycles. Although ubiquitous and abundant in marine ecosystems, little is known about their diversity and composition, which is usually affected by several environmental parameters. Due to their abundance and distribution, which includes shallow-water locations, the contribution of pockmarks to global methane and hydrocarbon release could be massive. Microbial assemblages associated with pockmarks are known to be different between active and inactive sites. In this study, the microbial assemblages associated with several pockmarks located at the outer shelf of the Estremadura Spur were revealed using a next-generation sequencing of the bacterial/archaeal 16S RRNA. The sampled stations show a similar community structure for the most abundant phyla. OTUs encompass 59 bacterial and three archaeal phyla. Within Bacteria, Proteobacteria with 62.6% was the dominant phylum followed by Actinobacteria (7.8%), Acidobacteria (7.7%), Bacteroidetes (4.5%) and Gemmatimonadetes (2.8%). These groups are known to dominate marine sediments and their diversity was comparable to other studies. The studied microbial assemblages also comprised several phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders emphasizing its importance for the ecosystem functioning.

scholarly journals Relationships between Environmental Factors and Pathogenic Vibrios in the Northern Gulf of Mexico

2010 ◽  
Vol 76 (21) ◽  
pp. 7076-7084 ◽  
Author(s):  
C. N. Johnson ◽  
A. R. Flowers ◽  
N. F. Noriea ◽  
A. M. Zimmerman ◽  
J. C. Bowers ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Water Column ◽  
Vibrio Vulnificus ◽  
Environmental Parameters ◽  
Sampling Period ◽  
Pathogenicity Factor ◽  
Hemolysin Gene ◽  
Thermostable Direct Hemolysin ◽  
Pathogenic Vibrios ◽  
Abundance And Distribution

ABSTRACT Although autochthonous vibrio densities are known to be influenced by water temperature and salinity, little is understood about other environmental factors associated with their abundance and distribution. Densities of culturable Vibrio vulnificus containing vvh (V. vulnificus hemolysin gene) and V. parahaemolyticus containing tlh (thermolabile hemolysin gene, ubiquitous in V. parahaemolyticus), tdh (thermostable direct hemolysin gene, V. parahaemolyticus pathogenicity factor), and trh (tdh-related hemolysin gene, V. parahaemolyticus pathogenicity factor) were measured in coastal waters of Mississippi and Alabama. Over a 19-month sampling period, vibrio densities in water, oysters, and sediment varied significantly with sea surface temperature (SST). On average, tdh-to-tlh ratios were significantly higher than trh-to-tlh ratios in water and oysters but not in sediment. Although tlh densities were lower than vvh densities in water and in oysters, the opposite was true in sediment. Regression analysis indicated that SST had a significant association with vvh and tlh densities in water and oysters, while salinity was significantly related to vibrio densities in the water column. Chlorophyll a levels in the water were correlated significantly with vvh in sediment and oysters and with pathogenic V. parahaemolyticus (tdh and trh) in the water column. Furthermore, turbidity was a significant predictor of V. parahaemolyticus density in all sample types (water, oyster, and sediment), and its role in predicting the risk of V. parahaemolyticus illness may be more important than previously realized. This study identified (i) culturable vibrios in winter sediment samples, (ii) niche-based differences in the abundance of vibrios, and (iii) predictive signatures resulting from correlations between environmental parameters and vibrio densities.

scholarly journals Micro-Landscape Dependent Changes in Arbuscular Mycorrhizal Fungal Community Structure

2021 ◽  
Vol 11 (11) ◽  
pp. 5297
Author(s):  
Stavros D. Veresoglou ◽  
Leonie Grünfeld ◽  
Magkdi Mola
Keyword(s):  
Community Structure ◽  
Mycorrhizal Fungi ◽  
Root Colonization ◽  
Environmental Parameters ◽  
Arbuscular Mycorrhizal ◽  
Fungal Community Structure ◽  
High Connectivity ◽  
Spatio Temporal ◽  
Arbuscular Mycorrhizal Fungal ◽  
Colonization Rates

The roots of most plants host diverse assemblages of arbuscular mycorrhizal fungi (AMF), which benefit the plant hosts in diverse ways. Even though we understand that such AMF assemblages are non-random, we do not fully appreciate whether and how environmental settings can make them more or less predictable in time and space. Here we present results from three controlled experiments, where we manipulated two environmental parameters, habitat connectance and habitat quality, to address the degree to which plant roots in archipelagos of high connectivity and invariable habitats are colonized with (i) less diverse and (ii) easier to predict AMF assemblages. We observed no differences in diversity across our manipulations. We show, however, that mixing habitats and varying connectivity render AMF assemblages less predictable, which we could only detect within and not between our experimental units. We also demonstrate that none of our manipulations favoured any specific AMF taxa. We present here evidence that the community structure of AMF is less responsive to spatio-temporal manipulations than root colonization rates which is a facet of the symbiosis which we currently poorly understand.

scholarly journals Effects of temperature on the behaviour and metabolism of an intertidal foraminifera and consequences for benthic ecosystem functioning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Noémie Deldicq ◽  
Dewi Langlet ◽  
Camille Delaeter ◽  
Grégory Beaugrand ◽  
Laurent Seuront ◽  
...  
Keyword(s):  
High Temperature ◽  
Ecosystem Functioning ◽  
Photosynthetic Activity ◽  
Species Traits ◽  
Biogeochemical Cycles ◽  
Variable Environment ◽  
Sediment Reworking ◽  
Temperature Regimes ◽  
Slow Moving ◽  
Effects Of Temperature

AbstractHeatwaves have increased in intensity, duration and frequency over the last decades due to climate change. Intertidal species, living in a highly variable environment, are likely to be exposed to such heatwaves since they can be emerged for more than 6 h during a tidal cycle. Little is known, however, on how temperature affects species traits (e.g. locomotion and behaviour) of slow-moving organisms such as benthic foraminifera (single-celled protists), which abound in marine sediments. Here, we examine how temperature influences motion-behaviour and metabolic traits of the dominant temperate foraminifera Haynesina germanica by exposing individuals to usual (6, 12, 18, 24, 30 °C) and extreme (high; i.e. 32, 34, 36 °C) temperature regimes. Our results show that individuals reduced their activity by up to 80% under high temperature regimes whereas they remained active under the temperatures they usually experience in the field. When exposed to a hyper-thermic stress (i.e. 36 °C), all individuals remained burrowed and the photosynthetic activity of their sequestered chloroplasts significantly decreased. Recovery experiments subsequently revealed that individuals initially exposed to a high thermal regime partially recovered when the hyper-thermic stress ceased. H. germanica contribution to surface sediment reworking substantially diminished from 10 mm3 indiv−1 day−1 (usual temperature) to 0 mm3 indiv−1 day−1 when individuals were exposed to high temperature regimes (i.e. above 32 °C). Given their role in sediment reworking and organic matter remineralisation, our results suggest that heatwaves may have profound long-lasting effects on the functioning of intertidal muddy ecosystems and some key biogeochemical cycles.

scholarly journals An evaluation of benthic community structure in and around the Sackville Spur closed area (Northwest Atlantic) in relation to the protection of vulnerable marine ecosystems

2012 ◽  
Vol 69 (2) ◽  
pp. 213-222 ◽  
Author(s):  
Christopher R. S. Barrio Froján ◽  
Kevin G. MacIsaac ◽  
Andrew K. McMillan ◽  
María del Mar Sacau Cuadrado ◽  
Philip A. Large ◽  
...  
Keyword(s):  
Community Structure ◽  
Benthic Community ◽  
Evaluation Process ◽  
Marine Ecosystems ◽  
Benthic Community Structure ◽  
Sponge Spicule ◽  
Northwest Atlantic ◽  
Depth Limit ◽  
Closed Area ◽  
Macrofaunal Community

Abstract Barrio Froján, C. R. S., MacIsaac, K. G., McMillan, A. K., del Mar Sacau Cuadrado, M., Large, P. A., Kenny, A. J., Kenchington, E., and de Cárdenas González,  E. 2012. An evaluation of benthic community structure in and around the Sackville Spur closed area (Northwest Atlantic) in relation to the protection of vulnerable marine ecosystems. – ICES Journal of Marine Science, 69: 213–222. The benthic macrofaunal community structure is investigated within and around a closed area at Sackville Spur in the Northwest Atlantic to ascertain whether continued exclusion of bottom fishing can be justified. This and other similar closed areas have been introduced by the Northwest Atlantic Fisheries Organisation (NAFO) to protect areas of likely occurrence of taxa that are indicative of vulnerable marine ecosystems (VMEs) from the damaging effects of bottom-contact fishing gear. Results reveal subtle yet significant differences in macrofaunal assemblage composition and community structure between inside and outside the closed area, between above and below the 1200-m depth contour (i.e. the historical depth limit of fishing), and between areas where dense sponge spicule mats are either present or absent. Differences were observed in many assemblage metrics; however, the most revealing was the greater abundance, biomass, diversity, and number of VME indicative taxa inside the closed area than outside. Overall community composition is also significantly different between treatments. Depth, sediment temperature, and the proportion of clay within sediments are important in shaping the faunal assemblage. The importance of the effects of fishing is discussed, although it is not possible to ascertain if fishing is the direct cause behind observed differences in the macrofaunal assemblage. A continued closure of the area is recommended, as well as options for streamlining the evaluation process of other closed areas.

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

scholarly journals Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

2021 ◽  
Vol 11 ◽  
Author(s):  
Emilie Darrigues ◽  
Benjamin W. Elberson ◽  
Annick De Loose ◽  
Madison P. Lee ◽  
Ebonye Green ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Next Generation Sequencing ◽  
Precision Medicine ◽  
Critical Role ◽  
First Year ◽  
Histopathological Diagnosis ◽  
Next Generation ◽  
Cancer Predisposition Syndrome ◽  
Generation Sequencing

Neuro-oncology biobanks are critical for the implementation of a precision medicine program. In this perspective, we review our first year experience of a brain tumor biobank with integrated next generation sequencing. From our experience, we describe the critical role of the neurosurgeon in diagnosis, research, and precision medicine efforts. In the first year of implementation of the biobank, 117 patients (Female: 62; Male: 55) had 125 brain tumor surgeries. 75% of patients had tumors biobanked, and 16% were of minority race/ethnicity. Tumors biobanked were as follows: diffuse gliomas (45%), brain metastases (29%), meningioma (21%), and other (5%). Among biobanked patients, 100% also had next generation sequencing. Eleven patients qualified for targeted therapy based on identification of actionable gene mutations. One patient with a hereditary cancer predisposition syndrome was also identified. An iterative quality improvement process was implemented to streamline the workflow between the operating room, pathology, and the research laboratory. Dedicated tumor bank personnel in the department of neurosurgery greatly improved standard operating procedure. Intraoperative selection and processing of tumor tissue by the neurosurgeon was integral to increasing success with cell culture assays. Currently, our institutional protocol integrates standard histopathological diagnosis, next generation sequencing, and functional assays on surgical specimens to develop precision medicine protocols for our patients. This perspective reviews the critical role of neurosurgeons in brain tumor biobank implementation and success as well as future directions for enhancing precision medicine efforts.

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