scholarly journals Gut Bacterial Communities of Dendroctonus valens and D. mexicanus (Curculionidae: Scolytinae): A Metagenomic Analysis across Different Geographical Locations in Mexico

2018 ◽  
Vol 19 (9) ◽  
pp. 2578 ◽  
Author(s):  
Juan Hernández-García ◽  
Roman Gonzalez-Escobedo ◽  
Carlos Briones-Roblero ◽  
Claudia Cano-Ramírez ◽  
Flor Rivera-Orduña ◽  
...  
Keyword(s):  
Central America ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Bark Beetles ◽  
Geographic Distance ◽  
Phylogenetic Distance ◽  
The Core ◽  
Dendroctonus Valens ◽  
Β Diversity ◽  
Geographical Locations

Dendroctonus bark beetles are a worldwide significant pest of conifers. This genus comprises 20 species found in North and Central America, and Eurasia. Several studies have documented the microbiota associated with these bark beetles, but little is known regarding how the gut bacterial communities change across host range distribution. We use pyrosequencing to characterize the gut bacterial communities associated with six populations of Dendroctonus valens and D. mexicanus each across Mexico, determine the core bacteriome of both insects and infer the metabolic pathways of these communities with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to evaluate whether these routes are conserved across geographical locations. Our results show that the β-diversity with UniFrac unweighted varies among locations of both bark beetles mainly due to absence/presence of some rare taxa. No association is found between the pairwise phylogenetic distance of bacterial communities and geographic distance. A strict intraspecific core bacteriome is determined for each bark beetle species, but these cores are different in composition and abundance. However, both bark beetles share the interspecific core bacteriome recorded previously for the Dendroctonus genus consisting of Enterobacter, Pantoea, Providencia, Pseudomonas, Rahnella, and Serratia. The predictions of metabolic pathways are the same in the different localities, suggesting that they are conserved through the geographical locations.

scholarly journals Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Pei Wang ◽  
Xiao Kong ◽  
Hongsong Chen ◽  
Youlun Xiao ◽  
Huijun Liu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rice Cultivars ◽  
Rice Varieties ◽  
Microbial Network ◽  
Β Diversity ◽  
Group I ◽  
Α Diversity ◽  
Microbe Interactions ◽  
Endophytic Bacterial Community ◽  
Group Ii

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.

An evaluation of the core bacterial communities associated with hypersaline environments in the Qaidam Basin, China

2020 ◽  
Vol 202 (8) ◽  
pp. 2093-2103 ◽  
Author(s):  
Derui Zhu ◽  
Rui Han ◽  
Qifu Long ◽  
Xiang Gao ◽  
Jiangwa Xing ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Qaidam Basin ◽  
Hypersaline Environments ◽  
The Core

scholarly journals Diversity of Soil Bacterial Community Is Influenced by Spatial Location and Time but Not Potato Cultivar

2020 ◽  
Vol 4 (3) ◽  
pp. 225-238
Author(s):  
Kamrun Nahar ◽  
Jean-Baptiste Floc’h ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sean Whitney
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Potato Cultivar ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Streptomyces Spp ◽  
Β Diversity ◽  
Soil Bacterial ◽  
Spatial Locations

Potato cultivars susceptible to common scab were previously reported to harbor five to six times more abundant pathogenic Streptomyces spp. in the rhizosphere soils compared with tolerant cultivars. It is still unclear if the diversity of soil bacterial communities is related to the abundance of pathogenic Streptomyces spp. This study evaluated the effects of potato cultivar on the diversity of bacterial communities in three spatial locations (soil located close to the plant [SCP], in the rhizosphere soil [RS], and in the geocaulosphere soil [GS]) in 2013 and 2014. Common scab tolerant (Goldrush and Hindenburg) and susceptible cultivars (Green Mountain and Agria) were planted in a field infested with pathogenic Streptomyces spp. causing common scab. The β-diversity of the bacterial community was significantly different between years and on dates within each year according to a permutational multivariate analysis of variance. The β-diversity also varied significantly among spatial locations (i.e., SCP, RS, and GS), probably due to changes in soil properties, but did not change significantly among potato cultivars. The architecture of the bacterial network in RS in 2014 was more complex compared with 2013 with a 2.5-fold increase in the number of bacteria included according to a co-occurrence analysis. These results indicated that the soil bacterial community diversity changed temporally and spatially. However, bacterial community diversity and richness were not affected by potato cultivar, suggesting that there were no relationships between bacterial community diversity or richness and the abundance of pathogenic Streptomyces spp.

Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs

2018 ◽  
Vol 64 (10) ◽  
pp. 732-743
Author(s):  
Huan Qu ◽  
Yanjie Huang ◽  
Yinghao Shi ◽  
Ying Liu ◽  
Shenglong Wu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Growth And Development ◽  
Intestinal Microflora ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Finishing Pigs ◽  
Rrna Gene Sequencing ◽  
Bacteria Communities

This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing–finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing–finishing pigs were randomly allocated to five diet groups: 0%, 0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. The addition of 1.5% bamboo vinegar powder had an effect on the intestinal microflora most similar to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicutes/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

scholarly journals Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph Methylomicrobium buryatense 5GB1

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Yanfen Fu ◽  
Lian He ◽  
Jennifer Reeve ◽  
David A. C. Beck ◽  
Mary E. Lidstrom
Keyword(s):  
Flux Balance Analysis ◽  
Metabolic Pathways ◽  
Scale Model ◽  
Obligate Methylotroph ◽  
Content Type ◽  
Advantages And Disadvantages ◽  
The Core ◽  
Flux Balance ◽  
Balance Analysis ◽  
Core Metabolism

ABSTRACT Methylomicrobium buryatense 5GB1 is an obligate methylotroph which grows on methane or methanol with similar growth rates. It has long been assumed that the core metabolic pathways must be similar on the two substrates, but recent studies of methane metabolism in this bacterium suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach and a 13C tracer approach were taken to understand core carbon metabolism in M. buryatense 5GB1 during growth on methanol and to determine whether such differences occur. Our results suggest a systematic shift of active core metabolism in which increased flux occurred through both the Entner-Doudoroff (ED) pathway and the partial serine cycle, while the tricarboxylic acid (TCA) cycle was incomplete, in contrast to growth on methane. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol, and the results are consistent with predictions based on ATP and NADH changes. Transcriptomics analysis suggested that the changes in fluxes and metabolite levels represented results of posttranscriptional regulation. The combination of flux balance analysis of the genome-scale model and the flux ratio from 13C data changed the solution space for a better prediction of cell behavior and demonstrated the significant differences in physiology between growth on methane and growth on methanol. IMPORTANCE One-carbon compounds such as methane and methanol are of increasing interest as sustainable substrates for biological production of fuels and industrial chemicals. The bacteria that carry out these conversions have been studied for many decades, but gaps exist in our knowledge of their metabolic pathways. One such gap is the difference between growth on methane and growth on methanol. Understanding such metabolism is important, since each has advantages and disadvantages as a feedstock for production of chemicals and fuels. The significance of our research is in the demonstration that the metabolic network is substantially altered in each case and in the delineation of these changes. The resulting new insights into the core metabolism of this bacterium now provide an improved basis for future strain design.

scholarly journals Bacterial colonization and succession in a newly opened hospital

2017 ◽  
Vol 9 (391) ◽  
pp. eaah6500 ◽  
Author(s):  
Simon Lax ◽  
Naseer Sangwan ◽  
Daniel Smith ◽  
Peter Larsen ◽  
Kim M. Handley ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Communities ◽  
Bacterial Colonization ◽  
Dynamic Bayesian Network ◽  
Hospital Staff ◽  
Hospital Environment ◽  
Temporal Correlations ◽  
Β Diversity ◽  
Bacterial Dynamics ◽  
Surgical Recovery

The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room. Bacterial communities on patients and room surfaces became increasingly similar over the course of a patient’s stay. Temporal correlations in community structure demonstrated that patients initially acquired room-associated taxa that predated their stay but that their own microbial signatures began to influence the room community structure over time. The α- and β-diversity of patient skin samples were only weakly or nonsignificantly associated with clinical factors such as chemotherapy, antibiotic usage, and surgical recovery, and no factor except for ambulatory status affected microbial similarity between the microbiotas of a patient and their room. Metagenomic analyses revealed that genes conferring antimicrobial resistance were consistently more abundant on room surfaces than on the skin of the patients inhabiting those rooms. In addition, persistent unique genotypes ofStaphylococcusandPropionibacteriumwere identified. Dynamic Bayesian network analysis suggested that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse but that there were no universal patterns of transmission across patient rooms.

Genetic variation and dispersal patterns in three varieties of Pinus caribaea (Pinaceae) in the Caribbean Basin

2018 ◽  
Vol 151 (1) ◽  
pp. 61-76
Author(s):  
Virginia Rebolledo Camacho ◽  
Lev Jardón Barbolla ◽  
Ivón Ramírez Morillo ◽  
Alejandra Vázquez-Lobo ◽  
Daniel Piñero ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Central America ◽  
Migration Rate ◽  
Geographic Distance ◽  
Caribbean Basin ◽  
Pinus Caribaea ◽  
The Bahamas ◽  
Geological Processes ◽  
The Caribbean

Background – Pinus caribaea Morelet comprises three varieties of tropical pines distributed in the Caribbean Basin: P. caribaea var. hondurensis, var. caribaea, and var. bahamensis. The insular and continental distribution of these varieties, as well as the geological processes in the region, have been important factors for analysing evolutionary processes implicated in the diversification of these lineages. In this study, we evaluate the genetic and geographic structure within and between these three varieties in order to infer the possible origin and dispersal routes of these taxa.Methods – We used six polymorphic nuclear microsatellites (nSSR) in fifteen representative populations of the three pine varieties, sampled throughout their natural range in Central America, Cuba and the Bahamas islands.Results – The varieties contain similar levels of genetic variation (mean He = 0.571), with several populations out of Hardy-Weinberg equilibrium, and significant levels of inbreeding (0.097–0.184, P ≤ 0.05). A slight but significant genetic differentiation was found between the varieties (RST = 0.088) and populations (RST= 0.082), and genetic differentiation increased with geographic distance (r2 = 0.263). Distance and Bayesian BAPS analyses generated seven groups; two represented by the two island varieties and the remainder by the Central American populations of var. hondurensis. Migration rate estimates between pairs of groups ranged from M = 0.47 to M = 20.16. Estimates were generally higher from the continent to islands, with the highest migration rate estimated from a continental genetic group to the Cuba island group of var. hondurensis (M = 20.16).Conclusions – This study supports the hypothesis of a recent origin of these pine taxa through the migration of an ancestor from Central America, where the historical demography is associated with events of colonization, expansion and contraction of populations. The genetic variation and differentiation suggest that the three varieties are divergent lineages that currently share allelic variants, indicating that their speciation has not yet completed.

scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

scholarly journals Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres

2020 ◽  
Author(s):  
Regina B. Bledsoe ◽  
Carol Goodwillie ◽  
Ariane L. Peralta
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Nutrient Enrichment ◽  
Bacterial Communities ◽  
Nutrient Addition ◽  
Soil Microbiome ◽  
The Core ◽  
Soil Bacterial

ABSTRACTIn nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast growing copiotrophs, slow growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized vs. unfertilized) and plant association (bulk vs. rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass vs. forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease suppressive bacterial taxa and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.ImportanceOver the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorous deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline and bacterial communities are anticipated to increase in abundance of copiotrophic taxa. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly, of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter the metabolism of rhizosphere bacterial communities in unexpected ways.

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