Canopy soil bacterial communities altered by severing host tree limbs

PeerJ ◽

10.7717/peerj.3773 ◽

2017 ◽

Vol 5 ◽

pp. e3773 ◽

Cited By ~ 4

Author(s):

Cody R. Dangerfield ◽

Nalini M. Nadkarni ◽

William J. Brazelton

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Forest Floor ◽

Soil Bacteria ◽

Forest Canopy ◽

Evolutionary Dynamics ◽

Host Tree ◽

16S Rrna Genes ◽

Rrna Genes ◽

Canopy Soil

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

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Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest

10.1101/094987 ◽

2016 ◽

Author(s):

Cody R. Dangerfield ◽

Nalini M. Nadkarni ◽

William J. Brazelton

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Forest Floor ◽

Soil Bacteria ◽

Host Tree ◽

Temperate Rainforest ◽

Living Tree ◽

Canopy Soil ◽

Unique Nature ◽

Temperate Rainforests

ABSTRACTTrees of temperate rainforests host a large biomass of epiphytes, living plants associated with soils formed in the forest canopy. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different species-level operational taxonomic units. A field experiment was conducted to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, connection to the living tree is an important factor in the ecology of canopy soil bacteria. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.IMPORTANCETemperate rainforests host large accumulations of epiphytes, plants that live on the branches of trees. This study provides a first look at the unique nature of bacterial communities in soil that is formed by the decomposition of epiphytes in the canopy of a temperate rainforest. Falling of epiphytic material results in the transfer of significant amounts of carbon and nutrients from the canopy to the forest floor. This study also experimentally documented how soil bacterial communities are affected by their movement from the canopy to the forest floor. The bacterial composition of canopy soil was altered by the severing of the epiphytic material from the living tree, even when the epiphytes remained in the canopy. Therefore, the unique nature of canopy soil bacteria is determined in part by the living host tree and not only by the physical environmental conditions associated with the canopy.

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Low Temperature (15 °C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea

Microorganisms ◽

10.3390/microorganisms7100475 ◽

2019 ◽

Vol 7 (10) ◽

pp. 475 ◽

Cited By ~ 1

Author(s):

Xiuling Wang ◽

Shunjie Liu ◽

Mingjie Chen ◽

Changxia Yu ◽

Yan Zhao ◽

...

Keyword(s):

High Temperature ◽

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Volvariella Volvacea ◽

Straw Mushroom ◽

Clustering Effect ◽

Relative Abundances

Straw mushroom (Volvariella volvacea) is the most commonly cultivated edible fungus in the world, but the challenges associated with the preservation have limited its marketability. Microbiology, especially bacteria, play a key role in the deterioration of food, this study aimed to reveal the succession of the bacterial community on the surfaces of V. volvacea fruit bodies under different temperature conditions. We amplified 16S rRNA genes of V4 regions, obtained the bacterial species information by using high-throughput sequencing technology, and analyzed the effects of environmental temperature and preservation time on bacterial communities. The relative abundances of Firmicutes, Bacilli, and Bacillales increased significantly when straw mushrooms began to rot. Furthermore, the relative abundances of Paenibacillus, Lysinibacillus and Solibacillus, which belong to Bacillales, increased with the decay of straw mushroom. The Shannon and Simpson indices of V. volvacea stored at 30 °C were significantly higher than those of V. volvacea stored at 15 °C, which indicates that a high temperature contributes to the improvement in the species diversity. According to the linear discriminant analysis (LDA) effect size (LEfSe) results, the number of biomarkers in the 30 °C group (32, 42.11%) was significantly higher than that in the 15 °C group (17, 22.37%), indicating that a high temperature has a clustering effect on some bacterial communities. A Spearman correlation analysis showed that Pseudomonas, Stenotrophomonas and Solibacillus promoted the decay of straw mushroom. In conclusion, a high temperature increases the bacterial diversity on the straw mushroom surfaces and has a clustering effect on the bacterial communities. The bacterial community consisting of Firmicutes, Bacilli, Bacillales, Paenibacillus, Lysinibacillus, Pseudomonas, Stenotrophomonas and Solibacillus could promote the decay of straw mushroom, so new preservation materials research can focus on inhibiting anaerobic and decay-causing bacteria to prolong preservation time.

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Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host

Applied and Environmental Microbiology ◽

10.1128/aem.01226-14 ◽

2014 ◽

Vol 80 (17) ◽

pp. 5254-5264 ◽

Cited By ~ 264

Author(s):

Ji-Hyun Yun ◽

Seong Woon Roh ◽

Tae Woong Whon ◽

Mi-Ja Jung ◽

Min-Soo Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Developmental Stage ◽

Bacterial Diversity ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

Operational Taxonomic Units ◽

Insect Order ◽

Insect Gut

ABSTRACTInsects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (±97.7) OTUs per sample. The insect gut microbiota were dominated byProteobacteria(62.1% of the total reads, including 14.1%Wolbachiasequences) andFirmicutes(20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities.

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Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef System, Southwestern Gulf of Mexico

Microorganisms ◽

10.3390/microorganisms9030619 ◽

2021 ◽

Vol 9 (3) ◽

pp. 619

Author(s):

Citlali Rodríguez-Gómez ◽

Lorena María Durán-Riveroll ◽

Yuri B. Okolodkov ◽

Rosa María Oliart-Ros ◽

Andrea M. García-Casillas ◽

...

Keyword(s):

Water Column ◽

Bacterial Diversity ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Reef System ◽

Field Samples ◽

Family Level ◽

Bacterial Biodiversity ◽

Sar11 Clade

Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.

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Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

Microorganisms ◽

10.3390/microorganisms8111657 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1657

Author(s):

Abdul-Salam Juhmani ◽

Alessandro Vezzi ◽

Mohammad Wahsha ◽

Alessandro Buosi ◽

Fabio De Pascale ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Host Response ◽

Environmental Parameters ◽

16S Rrna Genes ◽

Rrna Genes ◽

Nutrient Concentrations ◽

Lagoon Of Venice ◽

Anthropogenic Stressors ◽

Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

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Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽

10.1128/msystems.00731-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 14

Author(s):

Matthew R. Olm ◽

Alexander Crits-Christoph ◽

Spencer Diamond ◽

Adi Lavy ◽

Paula B. Matheus Carnevali ◽

...

Keyword(s):

Bacterial Diversity ◽

Ribosomal Proteins ◽

Large Scale ◽

Bacterial Species ◽

Bacterial Genome ◽

16S Rrna Genes ◽

Rrna Genes ◽

Species Discrimination ◽

Bacterial Genomes ◽

Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

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Variability of the Sheep Lung Microbiota

Applied and Environmental Microbiology ◽

10.1128/aem.00540-16 ◽

2016 ◽

Vol 82 (11) ◽

pp. 3225-3238 ◽

Cited By ~ 27

Author(s):

Laura Glendinning ◽

Steven Wright ◽

Jolinda Pollock ◽

Peter Tennant ◽

David Collie ◽

...

Keyword(s):

Spatial Variability ◽

Dna Sequences ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Large Animal ◽

Local Factors ◽

Adult Sheep ◽

Sequencing Technologies ◽

Host Influence

ABSTRACTSequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n= 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota.IMPORTANCEUntil recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.

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