scholarly journals The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 446
Author(s):  
Sierra R. Athen ◽  
Shivangi Dubey ◽  
John A. Kyndt
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Soda Lake ◽  
Sulfur Cycle ◽  
Microbial Interactions ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Coastal Salt Marshes ◽  
Sulfur Bacteria ◽  
Photosynthetic Sulfur Bacteria

The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique inland salt marsh environment.

Coastal salt-marshes plant communities of the Salicornietea fruticosae class in Apulia (Italy)

Biologia ◽  
2014 ◽  
Vol 69 (1) ◽  
Author(s):  
Saverio Sciandrello ◽  
Valeria Tomaselli
Keyword(s):  
Salt Marsh ◽  
Plant Communities ◽  
Salt Marshes ◽  
Field Work ◽  
Salt Marsh Vegetation ◽  
Marsh Vegetation ◽  
Apulia Region ◽  
Coastal Salt Marshes ◽  
Ecological Features ◽  
Halocnemum Strobilaceum

AbstractAn overview of the salt-marsh herbland and scrub vegetation belonging to the class Salicornietea fruticosae Br.-Bl. et Tx. ex A. Bolòs y Vayreda 1950 in Apulia is presented. Data available from literature have been supplemented with original relevés performed in different locations of the Apulia region. On the basis of a total of 297 relevés, fifteen communities have been defined, according to the traditional phytosociological system based on dominant and/or diagnostic taxa. For comparison purposes, the salt-marsh vegetation has been classified using numerical methods. The results obtained show that most of the clusters correspond to specific associations, and confirm the division into vegetation alliances and orders. Numerical analysis also allowed us to assign the proper allocation of some associations and plant communities drawn from literature. Five alliances, with plant communities characterized by specific ecological features, have been discriminated: Sarcocornion alpini and Arthrocnemion glauci (lower marshes), Salicornion fruticosae (middle marshes), Inulion crithmoidis and Suaedion brevofoliae (upper marshes). In addition, during the field work, a population of Halocnemum strobilaceum (Arthrocnemo-Halocnemetum strobilacei), new record for the Apulia region, has been found.

scholarly journals Assessing Salt Marsh Vulnerability Using High-Resolution Hyperspectral Imagery

2020 ◽  
Vol 12 (18) ◽  
pp. 2938
Author(s):  
Sarah B. Goldsmith ◽  
Rehman S. Eon ◽  
Christopher S. Lapszynski ◽  
Gregory P. Badura ◽  
David T. Osgood ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Salt Marsh ◽  
Salt Marshes ◽  
Multiple Stressors ◽  
Hyperspectral Imagery ◽  
Spatial Scales ◽  
Spectral Response ◽  
Accurate Determination ◽  
Foliar Nitrogen ◽  
Coastal Salt Marshes

Change in the coastal zone is accelerating with external forcing by sea-level rise, nutrient loading, drought, and over-harvest, leading to significant stress on the foundation plant species of coastal salt marshes. The rapid evolution of marsh state induced by these drivers makes the ability to detect stressors prior to marsh loss important. However, field work in coastal salt marshes can be challenging due to limited access and their fragile nature. Thus, remote sensing approaches hold promise for rapid and accurate determination of marsh state across multiple spatial scales. In this study, we evaluated the use of remote sensing tools to detect three dominant stressors on Spartina alterniflora. We took advantage of a barrier island salt marsh chronosequence in Virginia, USA, where marshes of different ages and level of stressor exist side by side. We collected hyperspectral imagery of plants along with salinity, sediment redox potential, and foliar nitrogen content in the field. We also conducted a greenhouse study where we manipulated environmental conditions. We found that models developed for stressors based on plant spectral response correlated well with salinity and foliar nitrogen within the greenhouse and field data, but were not transferable from lab to field, likely due to the limited range of conditions explored within the greenhouse experiments and the coincidence of multiple stressors in the field. This study is an important step towards the development of a remote sensing tool for tracking of ecosystem development, marsh health, and future ecosystem services.

scholarly journals An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions

2020 ◽  
Author(s):  
Akintunde Emiola ◽  
Wei Zhou ◽  
Julia Oh
Keyword(s):  
Human Skin ◽  
De Novo ◽  
Microbial Interactions ◽  
Skin Microbiome ◽  
Metagenomic Sequencing ◽  
Interspecies Interactions ◽  
Microbial Composition ◽  
Healthy Human ◽  
Skin Site ◽  
Cutibacterium Acnes

ABSTRACTThe healthy human skin microbiome is shaped by skin site physiology, individual-specific factors, and is largely stable over time despite significant environmental perturbation. Studies identifying these characteristics used shotgun metagenomic sequencing for high resolution reconstruction of the bacteria, fungi, and viruses in the community. However, these conclusions were drawn from a relatively small proportion of the total sequence reads analyzable by mapping to known reference genomes. ‘Reference-free’ approaches, based on de novo assembly of reads into genome fragments, are also limited in their ability to capture low abundance species, small genomes, and to discriminate between more similar genomes. To account for the large fraction of non-human unmapped reads on the skin—referred to as microbial ‘dark matter’—we used a hybrid de novo and reference-based approach to annotate a metagenomic dataset of 698 healthy human skin samples. This approach reduced the overall proportion of uncharacterized reads from 42% to 17%. With our refined characterization, we revisited assumptions about the skin microbiome, and demonstrated higher biodiversity and lower stability, particularly in dry and moist skin sites. To investigate hypotheses underlying stability, we examined growth dynamics and interspecies interactions in these communities. Surprisingly, even though most skin sites were relatively stable, many dominant skin microbes, including Cutibacterium acnes and staphylococci, were actively growing in the skin, with poor or no relationship between growth rate and relative abundance, suggesting that host selection or interspecies competition may be important factors maintaining community homeostasis. To investigate other mechanisms facilitating adaptation to a specific skin site, we identified Staphylococcus epidermidis genes that are likely involved in stress response and provide mechanisms essential for growth in oily sites. Finally, horizontal gene transfer—another mechanism of competition by which strains may swap antagonistic or virulent coding regions—was relatively limited in healthy skin, but suggested exchange of different metabolic and environmental tolerance pathways. Altogether, our findings underscore the value of a combined reference-based and de novo approach to provide significant new insights into microbial composition, physiology, and interspecies interactions to maintain community homeostasis in the healthy human skin microbiome.

scholarly journals Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Max Kolton ◽  
José L Rolando ◽  
Joel E Kostka
Keyword(s):  
Salt Marsh ◽  
Spartina Alterniflora ◽  
Salt Marshes ◽  
Root Zone ◽  
The United States ◽  
Microbial Interactions ◽  
Tall Plant ◽  
Plant Phenotype ◽  
Selective Forces ◽  
Oxidation Chemistry

ABSTRACT Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant–microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction–oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.

Urbanization impacts on production and recruitment of Fundulus heteroclitus in salt marsh creeks

2020 ◽  
Vol 645 ◽  
pp. 187-204
Author(s):  
PJ Rudershausen ◽  
JA Buckel
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Fundulus Heteroclitus ◽  
Multiple Factor Analysis ◽  
Southeastern Usa ◽  
Density Dependent ◽  
Dependent Relationship ◽  
Juvenile Abundance ◽  
The Relationship ◽  
Throw Trap

It is unclear how urbanization affects secondary biological production in estuaries in the southeastern USA. We estimated production of larval/juvenile Fundulus heteroclitus in salt marsh areas of North Carolina tidal creeks and tested for factors influencing production. F. heteroclitus were collected with a throw trap in salt marshes of 5 creeks subjected to a range of urbanization intensities. Multiple factor analysis (MFA) was used to reduce dimensionality of habitat and urbanization effects in the creeks and their watersheds. Production was then related to the first 2 dimensions of the MFA, month, and year. Lastly, we determined the relationship between creek-wide larval/juvenile production and abundance from spring and abundance of adults from autumn of the same year. Production in marsh (g m-2 d-1) varied between years and was negatively related to the MFA dimension that indexed salt marsh; higher rates of production were related to creeks with higher percentages of marsh. An asymptotic relationship was found between abundance of adults and creek-wide production of larvae/juveniles and an even stronger density-dependent relationship was found between abundance of adults and creek-wide larval/juvenile abundance. Results demonstrate (1) the ability of F. heteroclitus to maintain production within salt marsh in creeks with a lesser percentage of marsh as long as this habitat is not removed altogether and (2) a density-dependent link between age-0 production/abundance and subsequent adult recruitment. Given the relationship between production and marsh area, natural resource agencies should consider impacts of development on production when permitting construction in the southeastern USA.

scholarly journals Topological and Morphological Controls on Morphodynamics of Salt Marsh Interiors

2021 ◽  
Vol 9 (3) ◽  
pp. 311
Author(s):  
Ben R. Evans ◽  
Iris Möller ◽  
Tom Spencer
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
East Coast ◽  
Marsh Surface ◽  
Coastal Environments ◽  
Coastal System ◽  
Morphological Segmentation ◽  
The Usa ◽  
The Uk ◽  
Over Time

Salt marshes are important coastal environments and provide multiple benefits to society. They are considered to be declining in extent globally, including on the UK east coast. The dynamics and characteristics of interior parts of salt marsh systems are spatially variable and can fundamentally affect biotic distributions and the way in which the landscape delivers ecosystem services. It is therefore important to understand, and be able to predict, how these landscape configurations may evolve over time and where the greatest dynamism will occur. This study estimates morphodynamic changes in salt marsh areas for a regional domain over a multi-decadal timescale. We demonstrate at a landscape scale that relationships exist between the topology and morphology of a salt marsh and changes in its condition over time. We present an inherently scalable satellite-derived measure of change in marsh platform integrity that allows the monitoring of changes in marsh condition. We then demonstrate that easily derived geospatial and morphometric parameters can be used to determine the probability of marsh degradation. We draw comparisons with previous work conducted on the east coast of the USA, finding differences in marsh responses according to their position within the wider coastal system between the two regions, but relatively consistent in relation to the within-marsh situation. We describe the sub-pixel-scale marsh morphometry using a morphological segmentation algorithm applied to 25 cm-resolution maps of vegetated marsh surface. We also find strong relationships between morphometric indices and change in marsh platform integrity which allow for the inference of past dynamism but also suggest that current morphology may be predictive of future change. We thus provide insight into the factors governing marsh degradation that will assist the anticipation of adverse changes to the attributes and functions of these critical coastal environments and inform ongoing ecogeomorphic modelling developments.

scholarly journals Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel R. Leadbeater ◽  
Nicola C. Oates ◽  
Joseph P. Bennett ◽  
Yi Li ◽  
Adam A. Dowle ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Molecular Mechanisms ◽  
Surface Sediments ◽  
Gene Profiling ◽  
Oxidative Enzymes ◽  
Lignocellulose Degradation ◽  
Rrna Gene ◽  
Enzymatic Mechanisms

Abstract Background Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. Results Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. Conclusions Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments.

Epibiosis on eggs and brooding care in the burrowing crab Chasmagnathus granulatus (Brachyura:Varunidae): comparison between mudflats and salt marshes

2007 ◽  
Vol 87 (4) ◽  
pp. 893-901 ◽  
Author(s):  
Paola V. Silva ◽  
Tomás A. Luppi ◽  
Eduardo D. Spivak
Keyword(s):  
Salt Marsh ◽  
Filamentous Fungi ◽  
Salt Marshes ◽  
Maternal Care ◽  
Spartina Densiflora ◽  
Incubation Chamber ◽  
Stage Of Development ◽  
Key Species ◽  
Burrowing Crab ◽  
Chasmagnathus Granulatus

Chasmagnathus granulatus is a semiterrestrial intertidal burrowing crab that inhabits both the unvegetated mudflats and the cordgrass (Spartina densiflora) salt marshes in Mar Chiquita Lagoon (Argentina), where it is considered the ecologically key species. The mass of C. granulatus eggs incubated by females is colonized by epibiotic micro-organisms and accumulates detritus. The type of epibionts that use eggs as a substrate, the infestation degree, the maternal care behaviour and the protection of the incubation chamber were compared between females living on mudflats and on Spartina-dominated areas. In both places, the epibiosis by bacteria and filamentous fungi and peritrichid colonial ciliate was significantly higher in the periphery than in the centre of the brood mass. The accumulation of detritus was higher in the periphery in mudflat females but not in salt marsh females. Moreover, the level of detritus was significantly higher in mudflat than in salt marsh females only in the periphery of the brood. The infestation level of bacteria and fungi, and peritrichids, increased throughout the embryonic development only in mudflat females. The periphery of the brood mass was significantly more contaminated in mudflat than in marsh females, while the central region of the brood mass did not differ between habitats. The pleopods were significantly more contaminated by bacteria and filamentous fungi and peritrichid colonial ciliates in premoult females than in postmoult females, independently from the collection site. The percentage of females with abnormal embryos was significantly higher in mudflats (26.7%) than in marshes (12.3%). Females with late embryos spent more time flapping the abdomen and probing the embryos with the chela. Non-ovigerous females did not perform specific maternal care activities. The volume of brood mass both in early or late stage of development is greater than that of the incubation chamber and, consequently, peripheral embryos are more exposed.

Coastal Salt Marshes

2020 ◽  
pp. 1-39
Author(s):  
Maria Sarika ◽  
Andreas Zikos
Keyword(s):  
Salt Marshes ◽  
Coastal Salt Marshes
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