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 Sample Dilution and Bacterial Community Composition Influence Empirical Leucine-to-Carbon Conversion Factors in Surface Waters of the World's Oceans

2015 ◽  
Vol 81 (23) ◽  
pp. 8224-8232 ◽  
Author(s):  
Eva Teira ◽  
Víctor Hernando-Morales ◽  
Francisco M. Cornejo-Castillo ◽  
Laura Alonso-Sáez ◽  
Hugo Sarmento ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Nucleic Acid Content ◽  
Carbon Conversion ◽  
Production Rates ◽  
Conversion Factors ◽  
Content Type ◽  
Carbon Production ◽  
The Impact

ABSTRACTThe transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu−1and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyllaconcentration, picocyanobacterial abundance (mostlyProchlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that bothProchlorococcusand HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean.

scholarly journals Fecal Bacterial Community of Allopatric Przewalski’s Gazelles and Their Sympatric Relatives

2021 ◽  
Vol 12 ◽  
Author(s):  
Ruoshuang Liu ◽  
Jianbin Shi ◽  
Susanne Shultz ◽  
Dongsheng Guo ◽  
Dingzhen Liu
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Ecological Factors ◽  
Ovis Aries ◽  
Host Community ◽  
Tibetan Sheep ◽  
Fecal Bacterial Community ◽  
The Impact

Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski’s gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski’s gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski’s gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski’s gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski’s gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski’s gazelle’s gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski’s gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.

scholarly journals The Impact of Land use on Bacterial Community Composition and Physicochemical Properties of Soil

2016 ◽  
Vol 13 (4) ◽  
pp. 2167-2176
Author(s):  
Ghobad Jalali ◽  
Amir Lakzian ◽  
Alireza Astaraei ◽  
Aliakbar Haddad- Mashadrizeh ◽  
Mehdi Azadvar ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Physicochemical Properties ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
The Impact ◽  
Properties Of Soil

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 Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China

2015 ◽  
Vol 81 (19) ◽  
pp. 6567-6576 ◽  
Author(s):  
Lihua Niu ◽  
Yi Li ◽  
Peifang Wang ◽  
Wenlong Zhang ◽  
Chao Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Elevation Gradient ◽  
Ammonia Nitrogen ◽  
Phosphorus Concentration ◽  
Total Phosphorus Concentration ◽  
Content Type ◽  
Bacterial Phyla ◽  
Operational Variables

ABSTRACTTo understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla.Betaproteobacteria,Bacteroidetes, andFirmicutesdisplayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations.

scholarly journals Geographic and Host-Associated Variations in Bacterial Communities on the Floret Surfaces of Field-Grown Broccoli

2018 ◽  
Vol 84 (8) ◽  
pp. e02837-17 ◽  
Author(s):  
Min-Soo Kim ◽  
Jin-Woo Bae ◽  
Eun-Jin Park
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Associated Factors ◽  
Bacterial Community Composition ◽  
Leafy Vegetables ◽  
Bacterial Populations ◽  
Content Type ◽  
Fresh Vegetables ◽  
Tree Fruits

ABSTRACT Fresh vegetables harbor diverse bacterial populations on their surfaces. However, information on this microbiota is limited to a few types of fresh vegetables, and little is known about how it varies with geography and host condition. Here, we analyzed bacterial communities on the floret surfaces of 66 field-grown broccoli collected from 22 farms in four farming regions of Jeju Island, South Korea, using 454 pyrosequencing of 16S rRNA amplicons, and we determined their relationships to farming region and host-associated factors. Geographic variations in bacterial community composition and diversity were observed among farming regions, which partly reflected their relative humidity and insolation. The most abundant phyla were Proteobacteria, followed by Actinobacteria, Firmicutes, and Bacteroidetes; core operational taxonomic units (OTUs) assigned to Pseudomonas, Acinetobacter, Oxalobacteraceae, Comamonadaceae, and Enterobacteriaceae contributed to the community differences. Bacterial community composition differed between immature and mature samples, with mature samples harboring higher bacterial diversity. In comparison with communities on other types of fresh vegetables and fruits, bacterial communities on broccoli florets were unique but more similar to those of ground vegetables than to those of tree fruits/vegetables. This study presents novel data on the variability of floret-associated bacterial populations of field-grown broccoli relative to environmental and host-associated factors.IMPORTANCE Fresh vegetables harbor diverse and complex bacterial populations on their surfaces. These indigenous bacteria may play a role in human and crop health; however, the diversity and variability of bacterial communities on fresh vegetables require further study. A popular crop of leafy vegetables, broccoli, is of great agricultural and industrial importance. This study provides a detailed description of the bacterial community composition and diversity on the surfaces of broccoli florets. The variability of bacterial communities is associated with the geographic location of farming sites and is affected by host growth and health. The bacterial communities specific to broccoli were identified and showed greater similarity to those found on ground vegetables than to those found on tree fruits/vegetables. This study presents novel data on the impact of environmental and host-associated conditions on the variability of floret-associated bacterial populations present on field-grown broccoli.

scholarly journals Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Huan Wang ◽  
Rong Zhu ◽  
Xiaolin Zhang ◽  
Yun Li ◽  
Leyi Ni ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Community ◽  
Species Composition ◽  
Community Composition ◽  
Bacterial Communities ◽  
Phytoplankton Community ◽  
Bacterial Community Composition ◽  
Free Living ◽  
The Impact ◽  
Abiotic Environmental Factors

Abstract Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.

From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Syrie M Hermans ◽  
Matthew Taylor ◽  
Gwen Grelet ◽  
Fiona Curran-Cournane ◽  
Hannah L Buckley ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Reference Sites ◽  
Functional Potential ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACT Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.

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.

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