scholarly journals Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping

2012 ◽  
Vol 79 (4) ◽  
pp. 1160-1170 ◽  
Author(s):  
Özgül İnceoğlu ◽  
Leo Simon van Overbeek ◽  
Joana Falcão Salles ◽  
Jan Dirk van Elsas
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Growth Stage ◽  
Bulk Soil ◽  
Community Structures ◽  
Content Type ◽  
Operating Range ◽  
Normal Operating ◽  
Moving Window Analysis ◽  
Gm Potato

ABSTRACTIn this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the generaArthrobacter,Streptomyces,Rhodanobacter, andDokdonellawere consistently found only at the flowering potato plants in both seasons, whereasRhodoplanesandSporosarcinawere observed only in the soil planted to barley.

scholarly journals Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

2016 ◽  
Vol 82 (9) ◽  
pp. 2751-2762 ◽  
Author(s):  
Christopher Staley ◽  
Michael J. Sadowsky
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Local Variation ◽  
Community Structures ◽  
Content Type ◽  
Sample Depth ◽  
Beach Sands ◽  
Important Basis

ABSTRACTRecent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P< 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P< 0.001), where freshwater sands had significantly higher abundances of taxa within theActinobacteria,Betaproteobacteria, andVerrucomicrobiathan marine environments. In contrast, marine sands harbored greater abundances ofGammaproteobacteriaandPlanctomycetes, and those from Florida had moreDeltaproteobacteriaandFirmicutes. Marine beaches had significantly different phylogenetic community structures (P≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P< 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment.IMPORTANCEThis study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives.

scholarly journals Tagging Frogs with Passive Integrated Transponders Causes Disruption of the Cutaneous Bacterial Community and Proliferation of Opportunistic Fungi

2014 ◽  
Vol 80 (15) ◽  
pp. 4779-4784 ◽  
Author(s):  
Rachael E. Antwis ◽  
Gerardo Garcia ◽  
Andrea L. Fidgett ◽  
Richard F. Preziosi
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Pathogenic Fungus ◽  
Fold Increase ◽  
Bacterial Strains ◽  
Opportunistic Fungi ◽  
Content Type ◽  
Pit Tagging

ABSTRACTSymbiotic bacterial communities play a key role in protecting amphibians from infectious diseases including chytridiomycosis, caused by the pathogenic fungusBatrachochytrium dendrobatidis. Events that lead to the disruption of the bacterial community may have implications for the susceptibility of amphibians to such diseases. Amphibians are often marked both in the wild and in captivity for a variety of reasons, and although existing literature indicates that marking techniques have few negative effects, the response of cutaneous microbial communities has not yet been investigated. Here we determine the effects of passive integrated transponder (PIT) tagging on culturable cutaneous microbial communities of captive Morelet's tree frogs (Agalychnis moreletii) and assess the isolated bacterial strains for anti-B. dendrobatidisactivityin vitro. We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase). Handling also caused a disruption the bacterial community, although to a lesser extent than PIT tagging. However, the effects of both tagging and handling were temporary, and after 2 weeks, the bacterial communities were similar to their original compositions. We also identify two bacterial strains that inhibitB. dendrobatidis, one of which increased in abundance on PIT-tagged frogs at 1 day postmarking, while the other was unaffected. These results show that PIT tagging has previously unobserved consequences for cutaneous microbial communities of frogs and may be particularly relevant for studies that intend to use PIT tagging to identify individuals involved in trials to develop probiotic treatments.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Microbiology ◽  
2021 ◽  
Vol 167 (10) ◽  
Author(s):  
Aarón Barraza ◽  
Juan J. Montes-Sánchez ◽  
M. Goretty Caamal-Chan ◽  
Abraham Loera-Muro
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Plant Communities ◽  
Large Intestine ◽  
Bacterial Communities ◽  
Sonoran Desert ◽  
Rainy Season ◽  
Native Plant ◽  
Content Type ◽  
Link Type

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

scholarly journals Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

2012 ◽  
Vol 78 (7) ◽  
pp. 2359-2366 ◽  
Author(s):  
Merritt G. Gillilland ◽  
John R. Erb-Downward ◽  
Christine M. Bassis ◽  
Michael C. Shen ◽  
Galen B. Toews ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Structural Heterogeneity ◽  
Ecological Succession ◽  
Rrna Gene ◽  
Gi Tract ◽  
Content Type ◽  
Germ Free ◽  
Over Time

ABSTRACTLittle is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by eitherEscherichiaorBacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a “pioneering” community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.

scholarly journals Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies

Agronomy ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 14 ◽  
Author(s):  
Yadong Yang ◽  
Peixin Wang ◽  
Zhaohai Zeng
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Hierarchical Cluster ◽  
Organic Manure ◽  
Community Structures ◽  
Long Term Effects ◽  
Inorganic Fertilizers ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Fertilization plays important roles in improving soil fertility and in increasing crop yield. Soil microbial communities are sensitive indicators of soil quality and health, which could be affected by fertilization strategy. However, our knowledge on how organic–inorganic fertilizers application affects soil bacterial communities remains largely poorly understood. In this study, we investigated the long-term effects of different organic–inorganic fertilization strategies: without fertilizer (CK), fertilizers NPK (CF), fertilizers NPK, plus 30% organic manure (CFM1), and fertilizers NPK plus 60% organic manure (CFM2) on soil bacterial communities in paddy fields. Results showed that the bacterial 16S ribosomal DNA (rDNA) gene abundances in treatments CF, CFM1, and CFM2 were 1.44, 1.54, and 1.28 times higher than that in CK and the ACE index in treatment CFM1 was 9.0% greater than that in treatment CFM2, respectively. Fertilization strategy significantly changed the relative abundance of Nitrospirae, Gemmatimonadetes, and unclassified bacteria at the phylum level and bacteria belonging to order Nitrospira, candidate bacterium SBR2076, unclassified bacteria, Syntrophobacterales, and Solibacterales at the order level, respectively. High organic–inorganic fertilizer application rates inhibited the growth of Nitrospirae by 20–35%, and stimulated the growth of Gemmatimonadetes by 14–77%, relative to the rest of the treatments, respectively. Hierarchical cluster and principal coordinate analysis (PCoA) showed that the fertilization strategy affected the bacterial community structures, and the organic–inorganic fertilized treatments possessed similar bacterial community structures. Furthermore, soil pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors altering the bacterial communities. Our results suggested that combined organic–inorganic fertilizers application increased soil nutrient contents and bacterial abundances, and this could be an optimized fertilization strategy in regulating soil bacterial communities for rice production.

scholarly journals Bacteria as Emerging Indicators of Soil Condition

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Syrie M. Hermans ◽  
Hannah L. Buckley ◽  
Bradley S. Case ◽  
Fiona Curran-Cournane ◽  
Matthew Taylor ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Soil Condition ◽  
Soil Types ◽  
Anthropogenic Activity ◽  
Content Type ◽  
Soil Ecosystems ◽  
The Impact

ABSTRACT Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCE The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.

scholarly journals Bacterial Communities of Two Parthenogenetic Aphid Species Cocolonizing Two Host Plants across the Hawaiian Islands

2011 ◽  
Vol 77 (23) ◽  
pp. 8345-8349 ◽  
Author(s):  
Ryan T. Jones ◽  
Alberto Bressan ◽  
April M. Greenwell ◽  
Noah Fierer
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Host Plants ◽  
Aphis Gossypii ◽  
Hawaiian Islands ◽  
Aphid Species ◽  
Content Type ◽  
Alpinia Purpurata ◽  
Melon Aphid ◽  
Aphid Populations

ABSTRACTAphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid,Aphis gossypii, and the cardamom aphid,Pentalonia caladii) cocolonizing two plant species (taro,Colocasia esculenta, and ginger,Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, andA. gossypiiharbored a more diverse bacterial community thanP. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants.

scholarly journals Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

2021 ◽  
Vol 87 (6) ◽  
Author(s):  
F. Fracchia ◽  
L. Mangeot-Peter ◽  
L. Jacquot ◽  
F. Martin ◽  
C. Veneault-Fourrey ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Laser Scanning Microscopy ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Confocal Laser ◽  
Community Members ◽  
Root Microbiome ◽  
Over Time

ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

scholarly journals Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

2014 ◽  
Vol 81 (2) ◽  
pp. 522-532 ◽  
Author(s):  
Wan-Ying Xie ◽  
Jian-Qiang Su ◽  
Yong-Guan Zhu
Keyword(s):  
Bacterial Community ◽  
Paddy Soil ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Content Type ◽  
Soil Ecosystems ◽  
Α Diversity ◽  
Floating Macrophytes

ABSTRACTThe phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We tookWolffia australianaas a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere ofW. australianaharbored considerably rich communities of bacteria, withProteobacteriaandBacteroidetesas the predominant phyla. The core microbiome in the phyllosphere contained genera such asAcidovorax,Asticcacaulis,Methylibium, andMethylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.

scholarly journals Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

2018 ◽  
Vol 84 (12) ◽  
pp. e02797-17 ◽  
Author(s):  
Dandi Hou ◽  
Zhi Lin ◽  
Runze Wang ◽  
Jun Ge ◽  
Shuai Wei ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sedum Alfredii ◽  
Cd Stress ◽  
Metal Hyperaccumulation ◽  
Content Type

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

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