scholarly journals Bacterial Community Structure of Acid-Impacted Lakes: What Controls Diversity?

2008 ◽  
Vol 74 (6) ◽  
pp. 1856-1868 ◽  
Author(s):  
Sascha F. Percent ◽  
Marc E. Frischer ◽  
Paul A. Vescio ◽  
Ellen B. Duffy ◽  
Vincenzo Milano ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Community Composition ◽  
The United States ◽  
Trophic Levels ◽  
Community Diversity ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Bacterioplankton Community ◽  
Bacterioplankton Communities

ABSTRACT Although it is recognized that acidification of freshwater systems results in decreased overall species richness of plants and animals, little is known about the response of aquatic microbial communities to acidification. In this study we examined bacterioplankton community diversity and structure in 18 lakes located in the Adirondack Park (in the state of New York in the United States) that were affected to various degrees by acidic deposition and assessed correlations with 31 physical and chemical parameters. The pH of these lakes ranged from 4.9 to 7.8. These studies were conducted as a component of the Adirondack Effects Assessment Program supported by the U.S. Environmental Protection Agency. Thirty-one independent 16S rRNA gene libraries consisting of 2,135 clones were constructed from epilimnion and hypolimnion water samples. Bacterioplankton community composition was determined by sequencing and amplified ribosomal DNA restriction analysis of the clone libraries. Nineteen bacterial classes representing 95 subclasses were observed, but clone libraries were dominated by representatives of the Actinobacteria and Betaproteobacteria classes. Although the diversity and richness of bacterioplankton communities were positively correlated with pH, the overall community composition assessed by principal component analysis was not. The strongest correlations were observed between bacterioplankton communities and lake depth, hydraulic retention time, dissolved inorganic carbon, and nonlabile monomeric aluminum concentrations. While there was not an overall correlation between bacterioplankton community structure and pH, several bacterial classes, including the Alphaproteobacteria, were directly correlated with acidity. These results indicate that unlike more identifiable correlations between acidity and species richness for higher trophic levels, controls on bacterioplankton community structure are likely more complex, involving both direct and indirect processes.

scholarly journals High Temporal but Low Spatial Heterogeneity of Bacterioplankton in the Chesapeake Bay

2007 ◽  
Vol 73 (21) ◽  
pp. 6776-6789 ◽  
Author(s):  
Jinjun Kan ◽  
Marcelino T. Suzuki ◽  
Kui Wang ◽  
Sarah E. Evans ◽  
Feng Chen
Keyword(s):  
Chesapeake Bay ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Community Composition ◽  
The United States ◽  
Rapid Screening ◽  
23S Rrna ◽  
Rrna Gene ◽  
Length Variation ◽  
Bacterioplankton Community

ABSTRACT Compared to freshwater and the open ocean, less is known about bacterioplankton community structure and spatiotemporal dynamics in estuaries, particularly those with long residence times. The Chesapeake Bay is the largest estuary in the United States, but despite its ecological and economic significance, little is known about its microbial community composition. A rapid screening approach, ITS (internal transcribed spacer)-LH (length heterogeneity)-PCR, was used to screen six rRNA operon (16S rRNA-ITS-23S rRNA) clone libraries constructed from bacterioplankton collected in three distinct regions of the Chesapeake Bay over two seasons. The natural length variation of the 16S-23S rRNA gene ITS region, as well as the presence and location of tRNA-alanine coding regions within the ITS, was determined for 576 clones. Clones representing unique ITS-LH-PCR sizes were sequenced and identified. Dramatic shifts in bacterial composition (changes within subgroups or clades) were observed for the Alphaproteobacteria (Roseobacter clade, SAR11), Cyanobacteria (Synechococcus), and Actinobacteria, suggesting strong seasonal variation within these taxonomic groups. Despite large gradients in salinity and phytoplankton parameters, a remarkably homogeneous bacterioplankton community was observed in the bay in each season. Stronger seasonal, rather than spatial, variation of the bacterioplankton population was also supported by denaturing gradient gel electrophoresis and LH-PCR analyses, indicating that environmental parameters with stronger seasonal, rather than regional, dynamics, such as temperature, might determine bacterioplankton community composition in the Chesapeake Bay.

scholarly journals Avian Breeding Season Diversity and Community Composition in Camden White Gum and Slash Pine Plantations

2021 ◽  
Author(s):  
Elizabeth J Messick ◽  
Christopher E Comer ◽  
Michael A Blazier ◽  
T Bently Wigley
Keyword(s):  
United States ◽  
Species Richness ◽  
Community Composition ◽  
Pinus Elliottii ◽  
The United States ◽  
Slash Pine ◽  
Planted Forests ◽  
Eucalyptus Plantation ◽  
Short Rotation Woody Crops ◽  
Eucalyptus Plantations

Abstract In the southern United States, some landowners have established plantations of eucalyptus (Eucalyptus spp.) and are managing them on short rotations (<15 years) to provide wood for fiber and other potential uses. Establishment of short-rotation woody crops dominated by nonnative species has implications for resident fauna in the United States that are largely unknown. We compared avifauna abundance, diversity, and community composition in newly established Camden white gum (Eucalyptus benthamii) plantations with slash pine (Pinus elliottii) plantations of the same age and height (one to two and six to seven years old, respectively) in southwestern Louisiana, USA. Species richness, diversity, and community composition in newly established eucalyptus plantations and six- to seven-year-old pines were similar. More birds were observed, and bird detections varied less in eucalyptus plantations. Indigo buntings (Passerina cyanea) and other shrub-associated species were detected more often in eucalyptus stands. In contrast, species that inhabit herbaceous-dominated communities, such as eastern meadowlarks (Sturnella magna), or that were associated with a dense graminoid community (e.g., Bachman’s sparrow [Peucaea aestivalis]) were detected less often in eucalyptus. Overall, breeding bird communities in eucalyptus plantations one to two years postestablishment differed little from plantations dominated by slash pine. Study Implications Compared with slash pine (Pinus elliottii Englem) plantations of similar age and height (one to two years and six to seven years old, respectively) we found one- to two-year-old eucalyptus (Eucalyptus benthamii Maiden & Cambage) plantations supported similar avian species richness and diversity to six- to seven-year-old pine stands. Furthermore, we found these eucalyptus plantations (E13) supported an avian community that was intermediate to similar aged pine (S13) and pine of similar height (S08). However, avian communities will likely change as eucalyptus plantations age (Christian et al. 1997). Continued monitoring and assessment of community composition, richness, and abundance is important for determining the magnitude of this change. Future investigations focused on nest success, fecundity, postfledging monitoring, and survivorship compared with other types of planted forests and native cover types would help us better understand eucalyptus plantation effects on avifauna demographics (Van Horne 1983, Martin 1998, Jones 2001, Wood et al. 2004, Sage et al. 2006, Riffell et al. 2011).

scholarly journals Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

2021 ◽  
Vol 12 ◽  
Author(s):  
Larissa Frühe ◽  
Verena Dully ◽  
Dominik Forster ◽  
Nigel B. Keeley ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Environmental Dna ◽  
Community Diversity ◽  
Rrna Gene ◽  
Local Conditions ◽  
Global Trends ◽  
Bacterial Taxon ◽  
Metabolic Properties

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

scholarly journals Fungal and Bacterial Diversity Patterns of Two Diversity Levels Retrieved From a Late Decaying Fagus sylvatica Under Two Temperature Regimes

2021 ◽  
Vol 11 ◽  
Author(s):  
Sarah Muszynski ◽  
Florian Maurer ◽  
Sina Henjes ◽  
Marcus A. Horn ◽  
Matthias Noll
Keyword(s):  
Species Richness ◽  
Bacterial Community ◽  
Mass Loss ◽  
Community Composition ◽  
Fagus Sylvatica ◽  
Temperature Regime ◽  
Community Diversity ◽  
Interaction Patterns ◽  
Temperature Regimes ◽  
Natural Diversity

Environmental fluctuations are a common occurrence in an ecosystem, which have an impact on organismic diversity and associated ecosystem services. The aim of this study was to investigate how a natural and a species richness-reduced wood decaying community diversity were capable of decomposing Fagus sylvatica dead wood under a constant and a fluctuating temperature regime. Therefore, microcosms with both diversity levels (natural and species richness-reduced) were prepared and incubated for 8 weeks under both temperature regimes. Relative wood mass loss, wood pH, carbon dioxide, and methane emissions, as well as fungal and bacterial community compositions in terms of Simpson‘s diversity, richness and evenness were investigated. Community interaction patterns and co-occurrence networks were calculated. Community composition was affected by temperature regime and natural diversity caused significantly higher mass loss than richness-reduced diversity. In contrast, richness-reduced diversity increased wood pH. The bacterial community composition was less affected by richness reduction and temperature regimes than the fungal community composition. Microbial interaction patterns showed more mutual exclusions in richness-reduced compared to natural diversity as the reduction mainly reduced abundant fungal species and disintegrated previous interaction patterns. Microbial communities reassembled in richness-reduced diversity with a focus on nitrate reducing and dinitrogen-fixing bacteria as connectors in the network, indicating their high relevance to reestablish ecosystem functions. Therefore, a stochastic richness reduction was followed by functional trait based reassembly to recover previous ecosystem productivity.

scholarly journals Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere

2010 ◽  
Vol 76 (24) ◽  
pp. 8117-8125 ◽  
Author(s):  
Paul J. Hunter ◽  
Paul Hand ◽  
David Pink ◽  
John M. Whipps ◽  
Gary D. Bending
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Population Diversity ◽  
Microbial Interactions ◽  
Soluble Carbohydrates ◽  
Rrna Gene ◽  
Species Variation ◽  
Clone Libraries ◽  
Microbe Interactions

ABSTRACT Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

scholarly journals Responses of community structure and diversity to nitrogen deposition and rainfall addition in contrasting steppes are ecosystem-dependent and dwarfed by year-to-year community dynamics

2019 ◽  
Vol 124 (3) ◽  
pp. 461-469 ◽  
Author(s):  
Xuejun Yang ◽  
Zhenying Huang ◽  
Ming Dong ◽  
Xuehua Ye ◽  
Guofang Liu ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Global Change ◽  
Nitrogen Deposition ◽  
Community Composition ◽  
Community Dynamics ◽  
Environmental Variability ◽  
The Other ◽  
Desert Steppe ◽  
Typical Steppe

Abstract Background and Aims Long-term studies to disentangle the multiple, simultaneous effects of global change on community dynamics are a high research priority to forecast future distribution of diversity. Seldom are such multiple effects of global change studied across different ecosystems. Methods Here we manipulated nitrogen deposition and rainfall at levels realistic for future environmental scenarios in three contrasting steppe types in Mongolia and followed community dynamics for 7 years. Key Results Redundancy analyses showed that community composition varied significantly among years. Rainfall and nitrogen manipulations did have some significant effects, but these effects were dependent on the type of response and varied between ecosystems. Community compositions of desert and meadow steppes, but not that of typical steppe, responded significantly to rainfall addition. Only community composition of meadow steppe responded significantly to nitrogen deposition. Species richness in desert steppe responded significantly to rainfall addition, but the other two steppes did not. Typical steppe showed significant negative response of species richness to nitrogen deposition, but the other two steppes did not. There were significant interactions between year and nitrogen deposition in desert steppe and between year and rainfall addition in typical steppe, suggesting that the effect of the treatments depends on the particular year considered. Conclusions Our multi-year experiment thus suggests that responses of community structure and diversity to global change drivers are ecosystem-dependent and that their responses to experimental treatments are dwarfed by the year-to-year community dynamics. Therefore, our results point to the importance of taking annual environmental variability into account for understanding and predicting the specific responses of different ecosystems to multiple global change drivers.

scholarly journals Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

2012 ◽  
Vol 78 (11) ◽  
pp. 3958-3965 ◽  
Author(s):  
Amy Koid ◽  
William C. Nelson ◽  
Amy Mraz ◽  
Karla B. Heidelberg
Keyword(s):  
Community Composition ◽  
18S Rrna ◽  
Northwest Pacific ◽  
Rrna Gene ◽  
Gene Transcript ◽  
Acid Extraction ◽  
Phylogenetic Groups ◽  
Northwest Pacific Ocean ◽  
Clone Libraries ◽  
Sequencing Platform

ABSTRACTEukaryotic marine microbes play pivotal roles in biogeochemical nutrient cycling and ecosystem function, but studies that focus on the protistan biogeography and genetic diversity lag-behind studies of other microbes. 18S rRNA PCR amplification and clone library sequencing are commonly used to assess diversity that is culture independent. However, molecular methods are not without potential biases and artifacts. In this study, we compare the community composition of clone libraries generated from the same water sample collected at the San Pedro Ocean Time Series (SPOTs) station in the northwest Pacific Ocean. Community composition was assessed using different cell lysis methods (chemical and mechanical) and the extraction of different nucleic acids (DNA and RNA reverse transcribed to cDNA) to build Sanger ABI clone libraries. We describe specific biases for ecologically important phylogenetic groups resulting from differences in nucleic acid extraction methods that will inform future designs of eukaryotic diversity studies, regardless of the target sequencing platform planned.

scholarly journals Regime Transition Shapes the Composition, Assembly Processes and Co-Occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake

2021 ◽  
Author(s):  
Xinyi Cao ◽  
Dayong Zhao ◽  
Lisa Röttjers ◽  
Karoline Faust ◽  
Hongjie Zhang
Keyword(s):  
Community Composition ◽  
Regime Shift ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Nutrient Concentrations ◽  
Rrna Gene ◽  
Network Clustering ◽  
Regime Transition ◽  
Bacterioplankton Community ◽  
Occurrence Pattern

Abstract At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR).To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community were observed under the regime shift. The alpha diversity of bacterioplankton community was observed to consistently and continuously decrease with the regime shift from MDR to PDR, while the beta diversity presents the opposite. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes first decreased and then increased again closer to the PDR, most likely as a consequence of differences in nutrient concentration. The topological properties of bacterioplankton co-occurrence networks along the regime shift differed, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift and could be represented by phosphorus concentrations as well as several indicator species.

scholarly journals Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250675
Author(s):  
Xiang Zheng ◽  
Qidi Zhu ◽  
Zhijun Zhou ◽  
Fangtong Wu ◽  
Lixuan Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Feeding Habits ◽  
Bacterial Community Composition ◽  
Critical Role ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Insect Gut

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

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