scholarly journals Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9612
Author(s):  
Tong Jia ◽  
Tingyan Guo ◽  
Baofeng Chai
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Imperata Cylindrica ◽  
Copper Tailings ◽  
Α Diversity ◽  
Degraded Ecosystems ◽  
And Function

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

scholarly journals Different Soil Salinity Imparts Clear Alteration In Rhizospheric Bacterial Community Dynamics In Rice And Peanut.

2021 ◽  
Author(s):  
Md Majharul Islam ◽  
Rajarshi Bhattacharya ◽  
Biraj Sarkar ◽  
Pulak Kumar Maiti ◽  
Shouvik Mahanty ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Host Plant ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Rhizospheric Soil ◽  
Bacterial Community Dynamics

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

scholarly journals Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

2015 ◽  
Vol 81 (10) ◽  
pp. 3460-3470 ◽  
Author(s):  
A. Corrigan ◽  
Marcel de Leeuw ◽  
Stéphanie Penaud-Frézet ◽  
Diliana Dimova ◽  
R. A. Murphy
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Functional Capability ◽  
Content Type ◽  
Mannan Oligosaccharide ◽  
Commercial Broiler ◽  
Level 3 ◽  
Strong Segregation ◽  
And Function

ABSTRACTThis study focused on identifying reproducible effects of dietary supplementation with a mannan oligosaccharide (MOS) on the broiler cecal bacterial community structure and function in a commercial production setting. Two separate trials, each with a control and a supplemented group, were carried out in the same commercial location and run concurrently. Approximately 10,000 birds from the same commercial hatchery were mirror imaged into each of four commercial broiler sheds and fed either a control or supplemented diet. Cecal contents were obtained on days 7, 21, and 35 posthatch from 12 randomly caught broilers from each group. Bacterial pyrosequencing was performed on all samples, with approximately 250,000 sequences obtained per treatment per time point. The predominant phyla identified at all three time points in both trials wereFirmicutes,Bacteroidetes,Proteobacteria,Actinobacteria, andTenericutes, representing >99% of all sequences. MOS supplementation altered the bacterial community composition from 7 days supplementation through 35 days supplementation.Bacteroidetesappeared to be replacingFirmicutesas a result of supplementation, with the most noticeable effects after 35 days. The effects of supplementation were reproducible across both trials. PICRUSt was used to identify differences between the functional potentials of the bacterial communities as a result of MOS supplementation. Using level 3 KEGG ortholog function predictions, differences between control and supplemented groups were observed, with very strong segregation noted on day 35 posthatch in both trials. This indicated that alterations of bacterial communities as a result of MOS are likely to alter the functional capability of the cecum.

scholarly journals The neglected part of the microbiome: Prophage TJ1 regulates the bacterial community of the metaorganism Hydra

2019 ◽  
Author(s):  
Janina Lange ◽  
Sebastian Fraune ◽  
Thomas C.G. Bosch ◽  
Tim Lachnit
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Colonization ◽  
Bacterial Community Composition ◽  
Broad Host Range ◽  
The Stability ◽  
And Function ◽  
Multicellular Organisms

AbstractMany multicellular organisms are closely associated with a specific bacterial community and therefore considered “metaorganisms”. Controlling the bacterial community composition is essential for the stability and function of metaorganisms, but the factors contributing to the maintenance of host specific bacterial colonization are poorly understood. Here we demonstrate that in Hydra the most dominant bacterial colonizer Curvibacter sp. is associated with an intact prophage which can be induced by different environmental stressors both in vitro and in vivo. Differences in the induction capacity of Curvibacter phage TJ1 in culture (in vitro) and on Hydra (in vivo) imply that the habitat of the prokaryotic host and/or bacterial frequency dependent factors influence phage inducibility. Moreover, we show that phage TJ1 features a broad host range against other bacterial colonizer and is directly capable to affect bacterial colonization on Hydra. From these results we conclude that prophages are hidden part of the microbiome interfering with bacteria-bacteria interactions and have the potential to influence the composition of host associated bacterial communities.

scholarly journals Influences of land reclamation on soil bacterial communities of abandoned salt pans in the Yellow River Delta

2021 ◽  
Author(s):  
Yihao Zhu ◽  
Xiliang Song ◽  
Xiaoli Liu ◽  
Weifeng Chen ◽  
Xuchang Niu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Physicochemical Properties ◽  
Soil Nutrients ◽  
Bacterial Communities ◽  
Land Reclamation ◽  
Bacterial Community Composition ◽  
Soil Physicochemical Properties ◽  
Salt Pans ◽  
Α Diversity ◽  
Relative Abundances

Reclamation has been widely accepted to restore abandoned lands. Most studies focused on the improvement of land reclamation in soil nutrients and microbial activities. However, the effects of reclamation time on bacterial communities of abandoned salt pans are still unclear. The object of this study is to: i) assess the successional change of soil physicochemical properties and bacterial communities in reclaimed abandoned salt pans with different reclamation histories, and ii) figure out the main limit factors on the improvement of soil quality in reclaimed abandoned salt pans. The soils in a farmland (RTBL) and six abandoned salt pans with 1 year (RT1), 2 years (RT2), 3 years (RT3), 4 years (RT4), 8 years (RT8), and 9 years (RT9) of reclamation were sampled to investigate the temporal variation of soil properties, heavy metal content, bacterial community composition, and diversity. Results showed that the soil bulk density (BD), total dissolved salt (SS), median particle size (MMAD) decreased with the increase of reclamation time, while soil nutrient (soil organic matter, total nitrogen, available phosphorus, available potassium) showed an opposite trend. The bacterial α-diversity increased first, then decrease. Land reclamation enhanced the relative abundances of Acidobacteria, Chloroflexi, and Actinobacteria but reduced the relative abundances of Proteobacteria, Gemmatimonadetes, and Bacteroidetes. Compared with RTBL, the soil nutrients and bacterial community structure in RT1, RT2, RT3, and RT4 showed a significant difference.Therefore, reclamation time is a vital driving force for restoring soil physicochemical properties and bacterial communities in abandoned

scholarly journals Different Soil Salinity Imparts Clear Alteration in Rhizospheric Bacterial Community Dynamics in Rice and Peanut.

2021 ◽  
Author(s):  
Md Majharul Islam ◽  
Rajarshi Bhattacharya ◽  
Biraj Sarkar ◽  
Pulak Kumar Maiti ◽  
Shouvik Mahanty ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Host Plant ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Rhizospheric Soil ◽  
Bacterial Community Dynamics

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

scholarly journals Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

2009 ◽  
Vol 75 (15) ◽  
pp. 5111-5120 ◽  
Author(s):  
Christian L. Lauber ◽  
Micah Hamady ◽  
Rob Knight ◽  
Noah Fierer
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Spatial Scales ◽  
Bacterial Community Composition ◽  
Phylogenetic Structure ◽  
Soil Bacterial Communities ◽  
Soil Bacterial Community Structure ◽  
Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

scholarly journals Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5508 ◽  
Author(s):  
Yan Li ◽  
Yan Kong ◽  
Dexiong Teng ◽  
Xueni Zhang ◽  
Xuemin He ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Community Diversity ◽  
Species Identity ◽  
Halostachys Caspica ◽  
Lycium Ruthenicum ◽  
Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Soil microbes and oxygen influence the changes in bacterial community composition during swine carcass decomposition

2021 ◽  
Author(s):  
Michelle Miguel ◽  
Seon Ho Kim ◽  
Sang Suk Lee ◽  
Yong Il Cho
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Soil Microbes ◽  
Close Association ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Decomposition Process ◽  
Metagenomic Sequencing ◽  
Unsterilized Soil

Abstract Background Carcass decomposition is influenced by various factors such as temperature, humidity, microorganisms, invertebrates, and scavengers. Soil microbes play a significant role in the decomposition process. In this study, we investigated the changes in the bacterial community during carcass decomposition in soil with an intact microbial community and soil which was sterilized decomposed with and without oxygen access using 16s rRNA metagenomic sequencing. Results Based on the 16S rRNA metagenomic sequencing, a total of 988 operational taxonomic units (OTUs) representing 16 phyla and 533 genera were detected. The bacterial diversity varied across the based on the alpha diversity indices. The bacterial composition in the unsterilized soil – aerobic condition (U_A) and unsterilized soil – anaerobic condition (U_An) set-ups have higher alpha diversity than the other burial set-ups. Beta diversity analysis revealed a close association in the samples according to the burial type and decomposition day. Firmicutes was the dominant phylum across all samples regardless of the burial type and decomposition day. The bacterial community composition changed throughout the decomposition process in all burial set-up. Meanwhile, the genus Bacillus dominated the bacterial community towards the end of decomposition period. Conclusions Our results showed that bacterial community composition changed during carcass decomposition and was affected by the soil and oxygen access, with microorganisms belonging to phylum Firmicutes dominating the community.

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