scholarly journals Temporal and Spatial Changes in Phyllosphere Microbiome of Acacia Trees Growing in Arid Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Ashraf Al Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Hana Dimerets ◽  
Michael Brandwein ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Air Temperature ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Keystone Species ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Arid Environments ◽  
Sequencing Platform ◽  
Acacia Species

Background: The evolutionary relationships between plants and their microbiomes are of high importance to the survival of plants in general and even more in extreme conditions. Changes in the plant's microbiome can affect plant development, growth, fitness, and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate, phenology, and seasonality on the epiphytic and endophytic microbiome of acacia trees. One hundred thirty-nine leaf samples were collected throughout the sampling year and were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform.Results: Epiphytic bacterial diversity indices (Shannon–Wiener, Chao1, Simpson, and observed number of operational taxonomic units) were found to be nearly double compared to endophyte counterparts. Epiphyte and endophyte communities were significantly different from each other in terms of the composition of the microbial associations. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species, but the canopy sides and sample months exhibited different diversity, whereas the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epiphyte and endophytes communities. Bacterial community compositions showed that Firmicutes dominate A. raddiana, and Proteobacteria dominate A. tortilis; these bacterial communities consisted of only a small number of bacterial families, mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities, respectively. Interestingly, ~60% of the obtained bacterial classifications were unclassified below family level (i.e., “new”).Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epiphyte and endophyte communities, highlighting the importance of climate change (precipitation, air temperature, and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

scholarly journals Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

2021 ◽  
Author(s):  
Ashraf Al-Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Hana Dimerets ◽  
Michael Brandwein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Air Temperature ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Keystone Species ◽  
Tree Canopy ◽  
Arid Environments ◽  
Acacia Tortilis ◽  
Acacia Species

Abstract Background: The evolutionary relationships and interactions between plants and their microbiomes are of high importance to the survival of plants in extreme conditions. Changes in the plant’s microbiome can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopy) and seasonality on the epiphytic and endophytic microbiomes associated with these two tree species. One hundred and thirty nine leaf samples were collected throughout the year and their microbial communities were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform.Results: Epiphytic bacterial diversity estimates (Shannon-Wiener, Chao1, Simpson and observed number of OTUs), were found to be nearly double compared to endophyte counterparts, in addition epi- and endophyte communities were significantly different from each other. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species but the canopy sides and sample months exhibited different diversity, while the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epi- and endophytes communities. Bacterial community compositions showed that Firmicutes dominate Acacia raddiana and Proteobacteria dominate Acacia tortilis; these bacterial communities only consisted of a small number of bacterial families mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities. Interestingly, about 60% of the obtained bacterial classification were unclassified below family level. Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epi- and endophytes, highlighting the importance of climate change (precipitation, air temperature and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

scholarly journals Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

2020 ◽  
Author(s):  
Ashraf Al-Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Hana Dimerets ◽  
Michael Brandwein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
Air Temperature ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Keystone Species ◽  
Arid Environments ◽  
Acacia Tortilis ◽  
Biotic Factor

Abstract Background: The evolutionary relationships between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees ( Acacia raddiana and Acacia tortilis ) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform. Results: our results showed amplifying V4 region of the 16S rDNA better presented the bacterial communities of both end and epiphytes of Acacia trees than V2, V3 and V5 regions of the 16S r DNA. When comparing the bacterial diversity of endo and epiphytes of the two acacia trees (shannon, choa1, PD and observed number of OTU’s), the epiphytes diversity indices showed about twice higher diversity compared to endophytes. The bacterial community compositions comparing both end and epiphytes were also significantly different. Interestingly, Acacia tortilis (umbral canopy shape) had a higher epiphytes bacterial diversity compared to Acacia raddiana, but were not statistically different. However the endophyte bacterial communities were significantly different compared to the two Acacia species (Firmicutes dominated Acacia raddiana and Proteobacteria dominated the Acacia tortilis ) . Alongside the biotic factor, Abiotic factors such as air temperature and precipitation also showed to significantly effect endo and epiphytes bacterial communities, while air humidity only affected the epiphytes bacterial communities.Conclusions: These results shed light on the unique desert phyllosphere microbiome in mitigating stress conditions highlighting the importance of epiphytic and endophytic microbial communities which are driven by different genotypic and abiotic factors. This paper also shows only a few bacteria species (OTUS’s) to dominate both epi and endophytes highlighting the importance of climate change (precipitation, Air temperature) in affecting arid land ecosystems where acacia trees are considered keystone species in many arid regions.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

scholarly journals Bacterial Diversity in Agricultural Soils during Litter Decomposition

2004 ◽  
Vol 70 (1) ◽  
pp. 468-474 ◽  
Author(s):  
Oliver Dilly ◽  
Jaap Bloem ◽  
An Vos ◽  
Jean Charles Munch
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Crop Residues ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Agricultural Soils ◽  
Diversity Indices ◽  
Bacterial Dna ◽  
Southern Germany ◽  
Substrate Quality

ABSTRACT Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.

Molecular bacterial diversity and distribution in waste from a steel plant

2008 ◽  
Vol 54 (12) ◽  
pp. 996-1005 ◽  
Author(s):  
Dulcecleide B. Freitas ◽  
Mariana P. Reis ◽  
Leandro M. Freitas ◽  
Paulo S. Assis ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Partial Length ◽  
16S Rdna Sequences ◽  
Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

scholarly journals Bacterial Diversity in the Intestinal Mucosa of Dysbiosis Diarrhea Mice Treated with Qiweibaizhu Powder

2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Cheng-Xing Long ◽  
Hao-Qing Shao ◽  
Cheng-Yu Luo ◽  
Rong Yu ◽  
Zhou-Jin Tan
Keyword(s):  
Bacterial Diversity ◽  
Intestinal Mucosa ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Scientific Basis ◽  
Miseq Sequencing ◽  
Model Group ◽  
Sequencing Platform ◽  
Rrna Sequencing ◽  
Bacterial Structure

The current research tried to explore the effect of Qiweibaizhu powder (QWBZP) on the bacterial diversity and community structure of the intestinal mucosa of dysbiosis diarrhea mice and provide a scientific basis for the efficacy of QWBZP on antibiotic-induced diarrhea. A dysbiosis diarrhea mouse model was constructed with broad-spectrum antibiotics through a mixture of cephradine capsules and gentamicin sulfate (23.33 mL·kg-1·d-1). Intestinal mucosa was collected, and DNA was extracted from each group. The bacterial characteristics in intestinal mucosa were analyzed by MiSeq sequencing based on the 16S rRNA sequencing platform. There were no significant differences in alpha diversity indices among the three groups. The sample distributions in both the normal and QWBZP groups were relatively concentrated, and the distance among individuals was close. However, an opposite result was obtained in the model group. Furthermore, the composition and abundance of species were similar between the normal group and the QWBZP group at both the phylum and genus levels. After treatment with QWBZP, the abundance of Lactobacillus increased, and Proteobacteria decreased, and the Firmicutes/Bacteroidetes ratio decreased to a normal level. Our results indicate that QWBZP can help repair mucosal bacterial structure and recover mucosal microbiota. Specifically, QWBZP increased the abundance of Lactobacillus and Bacteroidales S24-7 group norank.

scholarly journals Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisa Paruch ◽  
Adam M. Paruch ◽  
Hans Geir Eiken ◽  
Monica Skogen ◽  
Roald Sørheim
Keyword(s):  
16S Rrna ◽  
Seasonal Dynamics ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Seasonal Succession ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Water Ecosystem

Abstract Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.

scholarly journals Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in super arid environments

2020 ◽  
Author(s):  
Ashraf Al-Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Michael Brandwein ◽  
Yael Bar Lavan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Keystone Species ◽  
Arid Environments ◽  
Sequencing Platform ◽  
Spatial Changes ◽  
Tree Canopies ◽  
Different Seasons ◽  
Putative Marker ◽  
First Time ◽  
The Relationship

AbstractAlong the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform. Results show that endophytic, but not epiphytic, microbiome communities were different between the two acacia species. Endophytic, but not epiphytic, microbiome was affected by temporal changes (seasons) in air temperature. Acacia canopy microclimate was also found to have a significant effect on exosphere microbiome, with A. tortilis having a higher microbial diversity than A. raddiana with significantly different community compositions in different seasons.ImportanceThe evolutionary relationships and interactions between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. In this study, we explored the relationship between keystone desert trees and their microbiome along seasonal variation. These results shed light on the importance and uniqueness of desert phyllosphere microbiome. Although acacia trees are considered keystone species in many arid regions, to the best of our knowledge, this is the first time that microbial descriptors have been applied in these systems. This work constitutes a new approach to the assessment of these important trees and a stepping stone in the application of microbial communities as a putative marker in a changing environment.

scholarly journals Bacterial Diversity in Soil Surround Subterranean Termites-Damaged Wooden Buildings in Seonamsa Temple and Effect of the Termites on Bacterial Diversity in Humus Soil

2021 ◽  
Vol 37 (4) ◽  
pp. 357-361
Author(s):  
Young Hee Kim ◽  
Boa Lim ◽  
Jeung Min Lee ◽  
Jin Young Hong ◽  
Soo Ji Kim ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Illumina Miseq ◽  
Subterranean Termites ◽  
Bacterial Composition ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Humus Soil

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple’s soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple’s soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

scholarly journals Comparison of bacterial diversity and abundance between sexes of Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) from China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8411
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Small Body ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Dominant Bacteria

Background Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and the thelytokous parthenogenesis, low temperature resistance, protection in galls, generation overlap and small body of L. invasa contribute to its rapid invasion and population growth. However, the endosymbiotic bacterial composition, abundance and sex differences of L. invasa remain unclear. Therefore, this research aimed to identify the bacterial communities in L. invasa adults and compare them between the sexes of L. invasa lineage B. Results The Illumina MiSeq platform was used to compare bacterial community composition between females and males of L. invasa by sequencing the V3–V4 region of the 16S ribosomal RNA gene. A total of 1,320 operational taxonomic units (OTUs) were obtained. These OTUs were subdivided into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males were Rickettsia and Rhizobium, respectively. Conclusion The endosymbiotic bacteria of L. invasa females and males were highly diverse. There were differences in the bacterial community of L. invasa between sexes, and the bacterial diversity in male specimens was greater than that in female specimens. This study presents a comprehensive comparison of bacterial communities in L. invasa and these data will provide an overall view of the bacterial community in both sexes of L. invasa with special attention on sex-related bacteria.

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