scholarly journals Characterisation of Environmental Biofilms Colonising Wall Paintings of the Fornelle Cave in the Archaeological Site of Cales

2021 ◽  
Vol 18 (15) ◽  
pp. 8048
Author(s):  
Daniele De Luca ◽  
Paolo Caputo ◽  
Teresa Perfetto ◽  
Paola Cennamo
Keyword(s):  
Microbial Communities ◽  
Environmental Conditions ◽  
Intergenic Spacer ◽  
Environmental Parameters ◽  
Archaeological Site ◽  
Taxonomic Composition ◽  
Wall Paintings ◽  
Culture Independent ◽  
Cyanobacteria And Algae ◽  
Biofilm Structure

Caves present unique habitats for the development of microbial communities due to their peculiar environmental conditions. In caves decorated with frescoes, the characterization of microbial biofilm is important to better preserve and safeguard such artworks. This study aims to investigate the microbial communities present in the Fornelle Cave (Calvi Risorta, Caserta, Italy) and their correlation with environmental parameters. The cave walls and the wall paintings have been altered by environmental conditions and microbial activity. We first used light microscopy and scanning electron microscopy (SEM) and X-ray diffraction to characterise the biofilm structure and the mineral composition of substrata, respectively. Then, using both culture-dependent (Sanger sequencing) and culture-independent (automated ribosomal intergenic spacer analysis, ARISA) molecular methods, we demonstrated that the taxonomic composition of biofilms was different across the three substrata analysed and, in some cases, positively correlated with some environmental parameters. We identified 47 taxa in the biofilm samples, specifically 8 bacterial, 18 cyanobacterial, 14 algal and 7 fungal taxa. Fungi showed the highest number of ARISA types on the tuff rock, while autotrophic organisms (cyanobacteria and algae) on the frescoes exposed to light. This study confirms that caves constitute a biodiversity-rich environment for microbial taxa and that, in the presence of wall paintings, taxonomic characterization is particularly important for conservation and restoration purposes.

scholarly journals Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3246 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Sofie E. Voerman ◽  
Jenna M. Lang ◽  
John J. Stachowicz ◽  
Jonathan A. Eisen
Keyword(s):  
Microbial Communities ◽  
Zostera Marina ◽  
Sulfur Metabolism ◽  
Model Organism ◽  
Environmental Parameters ◽  
Taxonomic Composition ◽  
Point Of View ◽  
Sample Type ◽  
Significant Finding ◽  
Taxonomic Groups

Background Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.

scholarly journals Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental and anthropogenic factors

2020 ◽  
Author(s):  
Dalit Roth Rosenberg ◽  
Markus Haber ◽  
Joshua Goldford ◽  
Maya Lalzar ◽  
Dikla Aharoonovich ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Environmental Conditions ◽  
Heterotrophic Bacteria ◽  
Environmental Parameters ◽  
Metabolic Potential ◽  
Free Living ◽  
Size Fractions ◽  
Marine Microbial Communities

SummaryIn the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (two years) in the ultra-oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free-living vs particle-associated), followed by depth and finally season. The free-living (FL) community was taxonomically richer and more stable than the particle-associated (PA) one, which was characterized by recurrent “blooms” of heterotrophic bacteria such as Alteromonas and Ralstonia. The heterotrophic FL and PA communities were also correlated with different environmental parameters: depth and phytoplankton correlated with the FL population, whereas PA bacteria were correlated primarily with season. A significant part of the variability in community structure could not, however, be explained by the measured environmental parameters. The metabolic potential of the PA community, predicted from 16S amplicon data, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.Originality – Significance StatementMarine microbial populations are complex and dynamic, and the environmental drivers of the structure and function of these communities are mostly unclear. Specifically, marine microbial communities change over time, over depth and between particle-associated and free-living size fractions, yet the relative importance of each of these axes of variability is unclear. Our results highlight fundamentally different population dynamics between free-living and particle-associated marine bacteria: free living populations were more similar between seasons, whereas particle-associated populations were highly variable and exhibited “blooms” of specific clades of heterotrophic bacteria. We also suggest that the environmental conditions often measured as part of oceanographic cruises are not enough to explain most of the variability in microbial population structure. We speculate that organismal interactions and the presence of anthropogenic pollution may be also be important yet under-sampled drivers of oligotrophic marine microbial communities.

scholarly journals Effects of Bacterial Antibiotic Production on Rhizosphere Microbial Communities from a Culture-Independent Perspective

1998 ◽  
Vol 64 (12) ◽  
pp. 5020-5022 ◽  
Author(s):  
Eduardo A. Robleto ◽  
James Borneman ◽  
Eric W. Triplett
Keyword(s):  
Phaseolus Vulgaris ◽  
Microbial Communities ◽  
Antibiotic Production ◽  
Intergenic Spacer ◽  
Rhizobium Etli ◽  
Apparent Effect ◽  
Ribosomal Intergenic Spacer ◽  
Culture Independent

ABSTRACT The effects of antibiotic production on rhizosphere microbial communities of field-grown Phaseolus vulgaris were assessed by using ribosomal intergenic spacer analysis. Inoculum strains ofRhizobium etli CE3 differing only in trifolitoxin production were used. Trifolitoxin production dramatically reduced the diversity of trifolitoxin-sensitive members of the α subdivision of the class Proteobacteria with little apparent effect on most microbes.

Information support for expert evaluation of the states of the external environment

2020 ◽  
pp. 71-76
Author(s):  
Rasol Murtadha Najah
Keyword(s):  
Decision Making ◽  
Environmental Conditions ◽  
Fuzzy Inference ◽  
Environmental Parameters ◽  
Information Support ◽  
Expert Assessment ◽  
Fuzzy Variables ◽  
Decision Making Models ◽  
The Difference ◽  
State Of The Environment

This article discusses the application of methods to enhance the knowledge of experts to build a decision-making model based on the processing of physical data on the real state of the environment. Environmental parameters determine its ecological state. To carry out research in the field of expert assessment of environmental conditions, the analysis of known works in this field is carried out. The results of the analysis made it possible to justify the relevance of the application of analytical, stochastic models and models based on methods of enhancing the knowledge of experts — experts. It is concluded that the results of using analytical and stochastic objects are inaccurate, due to the complexity and poor mathematical description of the objects. The relevance of developing information support for an expert assessment of environmental conditions is substantiated. The difference of this article is that based on the analysis of the application of expert methods for assessing the state of the environment, a fuzzy logic adoption model and information support for assessing the environmental state of the environment are proposed. The formalization of the parameters of decision-making models using linguistic and fuzzy variables is considered. The formalization of parameters of decision-making models using linguistic and fuzzy variables was considered. The model’s description of fuzzy inference is given. The use of information support for environment state assessment is shown on the example of experts assessing of the land desertification stage.

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