Comparative analysis of the bacterial community of the Patagonian lichen Peltigera frigida and its soil substrate

2021 ◽  
Author(s):  
Diego Leiva ◽  
Fernando Fernández-Mendoza ◽  
José Acevedo ◽  
Margarita Carú ◽  
Martin Grube ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Symbiotic System ◽  
Forest Sites ◽  
Diverse Community ◽  
Unassigned Genus ◽  
Soil Substrates ◽  
Underlying Soil

<p>The lichen microbiome includes a diverse community of organisms, spanning widely across the bacterial tree of life. Lichens have been proposed to form partially open symbiotic systems, in which some microorganisms may be transmitted along within lichen propagules, while others are acquired from the surrounding environmental community.</p><p>In this survey, we discuss the extent to which the lichen microbiome is connected to that of its immediate substrate. For this we sampled ten specimens of the Patagonian foliose cyanolichen <em>Peltigera frigida</em> and their underlying soil substrates in two forest sites of the Coyhaique National Reserve (Aysén Region, Chile). Using 16S metabarcoding with primers that exclude cyanobacteria, we identified a significant taxonomic divergence between the bacterial communities of lichens and substrates.</p><p>At the Phylum level, Proteobacteria (37% of relative abundance) are most abundant within lichens, while soil substrates are dominated by Acidobacteriota (39%). At the Genus level, some bacteria are significantly more abundant in lichens, such as <em>Sphingomonas</em> (8% in lichens vs 0.2% in substrates) or an unassigned genus of Chitinophagaceae (10% vs 2%). Conversely, genera like the unassigned acidobacterial genus SCN-69-37 (0.9% vs 12%) are more abundant in substrates.</p><p>Overall, our results are consistent with the idea that lichens shape their microbiome obtaining components from various sources, including reproductive propagules and the substrate on which they grow. Further experimental and ecological approaches are needed to assess the contribution of these microorganisms to the fitness of the symbiotic system.</p><p>Funding: FONDECYT 1181510.</p>

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 Effects of ultraviolet radiation on the community structure and metabolic pathways of A2O process at Plateau environment

2021 ◽  
Author(s):  
Zong Yongchen ◽  
He Qiang ◽  
Guo Mingzhe ◽  
You Junhao ◽  
Zhang Dongyan
Keyword(s):  
Community Structure ◽  
Water Treatment ◽  
Bacterial Community ◽  
Ultraviolet Radiation ◽  
Relative Abundance ◽  
Ultraviolet Irradiation ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Bacterial Community Structure ◽  
Key Species

Abstract Water treatment ecosystem provides important habitats for various bacterial communities. However, the response mechanism of this ecosystem under ultraviolet rays is not yet clear. In the study, 16S rRNA gene sequencing is used to study the bacterial community structure and metabolic pathways under 5 samples of ultraviolet irradiation times. In general, the bacterial communities of the five samples are different, which indicates that the ultraviolet radiation time has an impact on the bacterial community structure. Analysis of driving factors shows that UV, COD, pH, TN and NH3-N have an impact on the relative abundance of key species. Key species under ultraviolet irradiation are Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and Chlamydiae, accounting for 96.69%ཞ98.30%, and ultraviolet irradiation has a significant inhibitory effect on the relative abundance. As the dominant bacterial phyla in Plateau environment, Chlamydiae is discovered for the first time. The network co-occurrence diagrams constructed under different ultraviolet radiation show that each sample is composed of three independent network diagrams. There are 6 common dominant phyla and 33 common dominant bacterial genera in each sample, which reveals that the structure of the ecosystem is composed of more similar microorganisms, rather than random phenomena. It also reflects the competitive relationship between species and the adaptability of bacteria to the environment. Through the analysis of metabolic pathways, it is found that the dominant metabolic pathways in high altitude habitats have certain changes under ultraviolet radiation. Further analysis of carbon, nitrogen and phosphorus metabolic pathways shows that the relative abundance of related metabolic pathways has a certain change, but the difference in metabolic maps is small, that is, the effect of ultraviolet radiation is mainly reflected in the relative abundance of metabolic pathways. These findings indicate that ultraviolet radiation in Plateau environment as an important influencing factor has an impact on microbial structure and metabolic pathways. This research provides an important theoretical basis for further understanding of water treatment ecosystem in Plateau environment, and also provides a new perspective for the development of water treatment ecosystem.

scholarly journals Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xu Jiang ◽  
Hui Ma ◽  
Qing-lei Zhao ◽  
Jun Yang ◽  
Cai-yun Xin ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Paddy Soil ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Available Phosphorus ◽  
Uncultured Bacterium ◽  
Ditch Sediment

AbstractAs an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.

scholarly journals Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter

2017 ◽  
Author(s):  
Quanchao Zeng ◽  
Yang Liu ◽  
Shaoshan An
Keyword(s):  
Bacterial Community ◽  
Litter Decomposition ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Terrestrial Ecosystems ◽  
Soil Bacterial Diversity ◽  
Litter Addition ◽  
Normal Quantity ◽  
Soil Bacterial ◽  
Litter Quantity

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems.

scholarly journals Variation in Near-Surface Airborne Bacterial Communities among Five Forest Types

Forests ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 561
Author(s):  
Jianbo Fang ◽  
Qiyu Dong ◽  
Weijun Shen ◽  
Xiaoling Liu ◽  
Ning Dou ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Plant Diversity ◽  
Soil Ph ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Mixed Forest ◽  
Airborne Bacteria ◽  
Forest Types ◽  
Near Surface

Airborne bacteria play important roles in air pollution, human health and biogeochemical cycles. However, their spatial variation and determinant factors in forest environments are poorly understood. In this study, we selected five forest types in the Liuxihe National Park, South China, to analyze how near-surface bacterial community structure is related to the forest community structure and soil physicochemical properties. The results indicated that the dominant communities were mainly constituted by seven bacterial genera of the phyla Proteobacteria (49.7%–55.4%) and Firmicutes (44.2%–49.8%), including Exiguobacterium (42.0%–46.4%), Citrobacter (20.7%–25.8%), Acinetobacter (20.1%–22.1%), and Pseudomonas (7.8%–8.9%) etc. However, differences in the composition and diversity of the airborne bacterial communities were evident among the five forests, especially with respect to the dominant taxa. The relative abundance of Enterococcus and Bacillus in coniferous and broad-leaved mixed forest (MF), broad-leaved mixed forest (BF), and pure Cunninghamia lanceolata forest (CL) was significantly higher than that of the other forests, while the relative abundance of Citrobacter was significantly lower. The relative abundance of Citrobacter, Acinetobacter, and Pseudomonas in Proteobacteria were significantly negatively correlated with plant diversity and acid phosphatase activity but positively correlated with soil pH and soil available potassium. Contrastingly, the correlation between the relative abundance of most genera of Firmicutes and the above environmental factors is just the opposite of that for Proteobacteria. We provide direct evidence that native plant communities in the middle stage of succession, compared to planted forests and forest open space, generally had higher airborne bacterial diversity. Airborne bacterial diversity showed a significantly positive correlation with plant diversity (p < 0.05). Over all, soil pH, soil available potassium, and soil available phosphorus contributed to a high rate of the diversity of the airborne bacterial community in near-surface, followed by the plant diversity of the arbor layer and the near-surface air temperature. These results extended our understanding of the ecological patterns of airborne bacteria in forest ecosystems.

scholarly journals Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter

2017 ◽  
Author(s):  
Quanchao Zeng ◽  
Yang Liu ◽  
Shaoshan An
Keyword(s):  
Bacterial Community ◽  
Litter Decomposition ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Terrestrial Ecosystems ◽  
Soil Bacterial Diversity ◽  
Litter Addition ◽  
Normal Quantity ◽  
Soil Bacterial ◽  
Litter Quantity

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems.

scholarly journals Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra

2019 ◽  
Author(s):  
Ingeborg J. Klarenberg ◽  
Christoph Keuschnig ◽  
Ana J. Russi Colmenares ◽  
Denis Warshan ◽  
Anne D. Jungblut ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
The Arctic ◽  
Gene Copy ◽  
Nitrogen Fixing ◽  
Moss Species

AbstractBacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses, an abundant plant group in Arctic ecosystems, harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of the moss microbiome. Here, we studied the total and potentially active bacterial community associated with Racomitrium lanuginosum, a common moss species in the Arctic, in response to 20-year in situ warming in an Icelandic heathland. We evaluated changes in moss bacterial community composition and diversity. Further, we assessed the consequences of warming for nifH gene copy numbers and nitrogen-fixation rates. Long-term warming significantly changed both the total and the potentially active bacterial community structure. The relative abundance of Proteobacteria increased, while the relative abundance of Cyanobacteria and Acidobacteria decreased. While warming did not affect nitrogen-fixation rates and nifH gene abundance, we did find shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and non-cyanobacterial diazotrophs increasing in relative abundance. Our data suggests that the moss microbial community and the potentially nitrogen-fixing taxa are sensitive to future warming.

scholarly journals The impacts of a biochar application on selected soil properties and bacterial communities in an Albic Clayic Luvisol

2020 ◽  
Vol 15 (No. 2) ◽  
pp. 85-92
Author(s):  
Chengsen Zhao ◽  
Qingqing Xu ◽  
Lin Chen ◽  
Xiaoqing Li ◽  
Yutian Meng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Soil Properties ◽  
Bulk Density ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Soil Layer ◽  
Total Carbon ◽  
Soil Bacterial

In this four-year study, we focused on the impacts of a biochar application on physicochemical soil properties (soil total carbon, total nitrogen, total potassium, total phosphorus, available nitrogen, available potassium, available phosphorus, pH, bulk density and moisture) and bacterial communities in an Albic Clayic Luvisol. The biochar was applied to plots only once with rates of 0, 10, 20 and 30 t/ha at the beginning of the experiment. The soil samples were collected from the surface (0–10 cm) and second depth (10–20 cm) soil layers after four years. The results showed that that the soil total carbon (TC) and pH increased, but the soil bulk density (BD) decreased with the biochar application. The soil bacterial sequences determined by the Illumina MiSeq method resulted in a decrease in the relative abundance of Acidobacteria, but an increase in the Actinobacteria with the biochar application. The bacterial diversity was significantly influenced by the biochar application. The nonmetric multidimensional scaling (NMDS) and canonical correspondence analysis (CCA) indicated that the soil bacterial community structure was affected by both the biochar addition and the soil depth. The Mantel test analysis indicated that the bacterial community structure significantly correlated to a soil with a pH (r = 0.525, P = 0.001), bulk density (r = 0.539, P = 0.001) and TC (r = 0.519, P = 0.002) only. In addition, most of the differences in the soil properties, bacterial relative abundance and community composition in the second depth soil layer were greater than those in the surface soil layer.

scholarly journals Different Responses of Soil Bacterial Communities to Nitrogen Addition in Moss Crust

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingwen Huang ◽  
Weiguo Liu ◽  
Xi-En Long ◽  
Yangyang Jia ◽  
Xiyuan Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Genes ◽  
N Addition ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Moss Crust

Bacterial communities in soil serve an important role in controlling terrestrial biogeochemical cycles and ecosystem processes. Increased nitrogen (N) deposition in Northwest China is generating quantifiable changes in many elements of the desert environment, but the impacts of N deposition, as well as seasonal variations, on soil bacterial community composition and structure are poorly understood. We used high-throughput sequencing of bacterial 16S rRNA genes from Gurbantünggüt Desert moss crust soils to study the impacts of N addition on soil bacterial communities in March, May, and November. In November, we discovered that the OTU richness and diversity of soil bacterial community dropped linearly with increasing N input. In November and March, the diversity of the soil bacterial community decreased significantly in the medium-N and high-N treatments. In May, N addition caused a substantial change in the makeup of the soil bacterial composition, while the impacts were far less apparent in November and March. Furthermore, the relative abundance of major bacterial phyla reacted non-linearly to N addition, with high-N additions decreasing the relative richness of Proteobacteria, Bacteroidetes, and Acidobacteria while increasing the relative abundance of Actinobacteria and Chloroflexi. We also discovered that seasonality, as characterized by changes in soil moisture, pH, SOC, and AK content, had a significant impact on soil bacterial communities. Significant variations in the makeup of the community were discovered at the phylum and genus levels throughout the various months. In May, the variety of soil bacterial community was at its peak. Further investigation showed that the decrease in soil bacterial diversity was mostly attributed to a drop in soil pH. These results indicated that the impact of N deposition on the soil bacterial community was seasonally dependent, suggesting that future research should evaluate more than one sample season at the same time.

scholarly journals Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3777 ◽  
Author(s):  
Quanchao Zeng ◽  
Yang Liu ◽  
Shaoshan An
Keyword(s):  
Bacterial Community ◽  
Litter Decomposition ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Terrestrial Ecosystems ◽  
Soil Bacterial Diversity ◽  
Litter Addition ◽  
Normal Quantity ◽  
Soil Bacterial ◽  
Litter Quantity

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems.

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