scholarly journals Comparative Analysis of the Ecological Succession of Microbial Communities on Two Artificial Reef Materials

2021 ◽  
Vol 9 (1) ◽  
pp. 120
Author(s):  
Zhansheng Guo ◽  
Lu Wang ◽  
Wei Cong ◽  
Zhaoyang Jiang ◽  
Zhenlin Liang
Keyword(s):  
Microbial Communities ◽  
Habitat Restoration ◽  
Artificial Reef ◽  
Shannon Index ◽  
Operational Taxonomic Units ◽  
Microbial Biofilms ◽  
Resource Enhancement ◽  
Temporal Succession ◽  
Concrete Operational ◽  
Over Time

Concrete and wood are commonly used to manufacture artificial reefs (ARs) worldwide for marine resource enhancement and habitat restoration. Although microbial biofilms play an important role in marine ecosystems, the microbial communities that colonize concrete and wooden ARs and their temporal succession have rarely been studied. In this study, the temporal succession of the microbial communities on concrete and wooden AR blocks and the driving factors were investigated. The composition of the microbial communities underwent successive shifts over time: among the six dominant phyla, the relative abundances of Proteobacteria, Cyanobacteria and Gracilibacteria significantly decreased in wood, as did that of Cyanobacteria in concrete. Operational taxonomic units (OTU) richness and Shannon index were significantly higher in concrete than in wood. Non-metric multidimensional scaling ordination placed the microbial communities in two distinct clusters corresponding to the two substrate materials. The macrobenthic compositions of concrete and wood were broadly similar and shifted over time, especially in the first five weeks. The Shannon index of the microbial communities in concrete and wood increased significantly with the organism coverage. The results provide fundamental data on microbial community succession during the initial deployment of ARs and contribute to understanding the ecological effects of ARs.

scholarly journals Molecular Analysis of Shower Curtain Biofilm Microbes

2004 ◽  
Vol 70 (7) ◽  
pp. 4187-4192 ◽  
Author(s):  
Scott T. Kelley ◽  
Ulrike Theisen ◽  
Largus T. Angenent ◽  
Allison St. Amand ◽  
Norman R. Pace
Keyword(s):  
Microbial Communities ◽  
Biofilm Formation ◽  
Environmental Dna ◽  
Rrna Genes ◽  
Opportunistic Pathogens ◽  
Microbial Biofilms ◽  
Potential Source ◽  
Household Environment ◽  
Soap Scum ◽  
Over Time

ABSTRACT Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as “soap scum,” which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the α-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.

scholarly journals Multicellular and unicellular responses of microbial biofilms to stress

2020 ◽  
Vol 401 (12) ◽  
pp. 1365-1374
Author(s):  
Daniel K.H. Rode ◽  
Praveen K. Singh ◽  
Knut Drescher
Keyword(s):  
Microbial Communities ◽  
Stress Responses ◽  
Spatial Scales ◽  
Organizational Level ◽  
Internal Stresses ◽  
Microbial Life ◽  
Microbial Biofilms ◽  
Applied Stresses

AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alberto Pascual-García
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Environmental Conditions ◽  
The Novel ◽  
Methodological Framework ◽  
Operational Taxonomic Units ◽  
Traditional Classification ◽  
Taxonomical Classification ◽  
Novel Concept

AbstractIn this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology.

scholarly journals Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
J. C. Madan ◽  
D. C. Koestler ◽  
B. A. Stanton ◽  
L. Davidson ◽  
L. A. Moulton ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Respiratory Tract ◽  
Microbial Communities ◽  
Effective Means ◽  
Significant Proportion ◽  
Gut Colonization ◽  
Pulmonary Damage ◽  
Chronic Colonization ◽  
High Degree ◽  
Over Time

ABSTRACT Pulmonary damage caused by chronic colonization of the cystic fibrosis (CF) lung by microbial communities is the proximal cause of respiratory failure. While there has been an effort to document the microbiome of the CF lung in pediatric and adult patients, little is known regarding the developing microflora in infants. We examined the respiratory and intestinal microbiota development in infants with CF from birth to 21 months. Distinct genera dominated in the gut compared to those in the respiratory tract, yet some bacteria overlapped, demonstrating a core microbiota dominated by Veillonella and Streptococcus. Bacterial diversity increased significantly over time, with evidence of more rapidly acquired diversity in the respiratory tract. There was a high degree of concordance between the bacteria that were increasing or decreasing over time in both compartments; in particular, a significant proportion (14/16 genera) increasing in the gut were also increasing in the respiratory tract. For 7 genera, gut colonization presages their appearance in the respiratory tract. Clustering analysis of respiratory samples indicated profiles of bacteria associated with breast-feeding, and for gut samples, introduction of solid foods even after adjustment for the time at which the sample was collected. Furthermore, changes in diet also result in altered respiratory microflora, suggesting a link between nutrition and development of microbial communities in the respiratory tract. Our findings suggest that nutritional factors and gut colonization patterns are determinants of the microbial development of respiratory tract microbiota in infants with CF and present opportunities for early intervention in CF with altered dietary or probiotic strategies. IMPORTANCE While efforts have been focused on assessing the microbiome of pediatric and adult cystic fibrosis (CF) patients to understand how chronic colonization by these microbes contributes to pulmonary damage, little is known regarding the earliest development of respiratory and gut microflora in infants with CF. Our findings suggest that colonization of the respiratory tract by microbes is presaged by colonization of the gut and demonstrated a role of nutrition in development of the respiratory microflora. Thus, targeted dietary or probiotic strategies may be an effective means to change the course of the colonization of the CF lung and thereby improve patient outcomes.

scholarly journals Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252216
Author(s):  
Laurie Dunn ◽  
Christophe Lang ◽  
Nicolas Marilleau ◽  
Sébastien Terrat ◽  
Luc Biju-Duval ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Soil Properties ◽  
Microbial Communities ◽  
Soil Microorganisms ◽  
Soil Microbial Communities ◽  
Partial Least Square ◽  
Farming Practices ◽  
Soil Microbial ◽  
Bacterial Richness ◽  
Over Time

According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.

scholarly journals Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Antoine Bagnaro ◽  
Federico Baltar ◽  
Gretchen Brownstein ◽  
William G. Lee ◽  
Sergio E. Morales ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Fuzzy Clustering ◽  
Water Mass ◽  
Rrna Gene ◽  
Microbial Ecosystem ◽  
Transition Zones ◽  
Ecosystem Boundaries ◽  
Operational Taxonomic Units ◽  
Pelagic Environment ◽  
Environmental Transitions

Abstract Background One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries. Results We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5 years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time. Conclusion We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.

scholarly journals Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 112 ◽  
Author(s):  
Abubakr Abdelwhab Hamd Elmagzob ◽  
Muhammed Mustapha Ibrahim ◽  
Guo-Fang Zhang
Keyword(s):  
16S Rdna ◽  
High Throughput Sequencing ◽  
Shannon Index ◽  
Ribosomal Database Project ◽  
Cinnamomum Camphora ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Endophytic Bacterial Community ◽  
Seasonal Diversity

Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.

scholarly journals Global airborne microbial communities controlled by surrounding landscapes and wind conditions

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Romie Tignat-Perrier ◽  
Aurélien Dommergue ◽  
Alban Thollot ◽  
Christoph Keuschnig ◽  
Olivier Magand ◽  
...  
Keyword(s):  
Particulate Matter ◽  
High Altitude ◽  
Microbial Communities ◽  
Atmospheric Chemistry ◽  
Sampling Site ◽  
Temporal Stability ◽  
Fungal Species ◽  
The World ◽  
Bacteria And Fungi ◽  
Over Time

Abstract The atmosphere is an important route for transporting and disseminating microorganisms over short and long distances. Understanding how microorganisms are distributed in the atmosphere is critical due to their role in public health, meteorology and atmospheric chemistry. In order to determine the dominant processes that structure airborne microbial communities, we investigated the diversity and abundance of both bacteria and fungi from the PM10 particle size (particulate matter of 10 micrometers or less in diameter) as well as particulate matter chemistry and local meteorological characteristics over time at nine different meteorological stations around the world. The bacterial genera Bacillus and Sphingomonas as well as the fungal species Pseudotaeniolina globaosa and Cladophialophora proteae were the most abundant taxa of the dataset, although their relative abundances varied greatly based on sampling site. Bacterial and fungal concentration was the highest at the high-altitude and semi-arid plateau of Namco (China; 3.56 × 106 ± 3.01 × 106 cells/m3) and at the high-altitude and vegetated mountain peak Storm-Peak (Colorado, USA; 8.78 × 104 ± 6.49 × 104 cells/m3), respectively. Surrounding ecosystems, especially within a 50 km perimeter of our sampling stations, were the main contributors to the composition of airborne microbial communities. Temporal stability in the composition of airborne microbial communities was mainly explained by the diversity and evenness of the surrounding landscapes and the wind direction variability over time. Airborne microbial communities appear to be the result of large inputs from nearby sources with possible low and diluted inputs from distant sources.

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