scholarly journals Spatial and Temporal Distribution of Soil Microbial Properties in Two Shrub Intercrop Systems of the Sahel

2021 ◽  
Vol 5 ◽  
Author(s):  
Sire Diedhiou-Sall ◽  
Komi B. Assigbetsee ◽  
Aminata N. Badiane ◽  
Ibrahima Diedhiou ◽  
M. Khouma ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Enzyme Activities ◽  
Temporal Dynamics ◽  
Dry Season ◽  
Hydraulic Lift ◽  
Annual Rainfall ◽  
Rrna Gene ◽  
28S Rrna ◽  
Microbial Composition ◽  
Row Crops

The Sahel is an ecologically vulnerable region where increasing populations with a concurrent increase in agricultural intensity has degraded soils. Agroforestry offers an approach to remediate these landscapes. A largely unrecognized agroforestry resource in the Sahel are the native shrubs, Piliostigma reticulatum, and Guiera senegalensis that to varying degrees already coexist with row crops. These shrubs improve soil quality, redistribute water from the deep soil to the surface (hydraulic lift), and can improve crop growth. However, little information is available on whether these shrubs affect spatial and temporal dynamics of microbial communities. Therefore, the objective of this study was to determine microbial composition and activity in the wet and dry seasons of soil in the: shrub rhizosphere (RhizS), inter-root zone (IntrS), and outside the influence of shrub soil (OutS) for both G. senegalensis and P. reticulatum in Senegal. A 3 × 2 factorial field experiment was imposed at two locations (490 and 700 mm annual rainfall with G. senegalensis and P. reticulatum, respectively), that had the soil sampling treatments of three locations (RhizS, IntrS, and OutS) and two seasons (wet and dry). Soils were analyzed for: microbial diversity (DGGE with bacterial 16S or fungal 28S rRNA gene sequences phospholipids fatty acid, PLFA); enzyme activities; microbial biomass carbon (MBC); and nitrogen (N) mineralization potential. For the DGGE profiling, the bacterial community responded more to the rhizosphere effect, whereas, the fungal community was more sensitive to season. PLFA, MBC, enzyme activities and inorganic N were significantly higher in both seasons for the RhizS. The presence of shrubs maintained rhizosphere microbial communities and activity during the dry season. This represents a paradigm shift for semi-arid environments where logically it would be expected to have no microbial activity in the extended dry season. In contrast this study has shown this is not the case that rather the presence of shrub roots maintained the microbial community in the dry season most likely due to hydraulic lift and root exudates. This has implications when these shrubs are in cropped fields in that decomposition and mineralization of nutrients can proceed in the dry season. Thus, enabling accumulation of plant available nutrients during the dry season for uptake by crops in the rainy season.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals Extracellular Enzyme Activity and Microbial Diversity Measured on Seafloor Exposed Basalts from Loihi Seamount Indicate the Importance of Basalts to Global Biogeochemical Cycling

2014 ◽  
Vol 80 (16) ◽  
pp. 4854-4864 ◽  
Author(s):  
Myrna E. Jacobson Meyers ◽  
Jason B. Sylvan ◽  
Katrina J. Edwards
Keyword(s):  
Enzyme Activity ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Leucine Aminopeptidase ◽  
Extracellular Enzyme ◽  
Basaltic Rock ◽  
Rrna Gene ◽  
Content Type ◽  
Shelf Sediments ◽  
Potential Enzyme Activity

ABSTRACTSeafloor basalts are widely distributed and host diverse prokaryotic communities, but no data exist concerning the metabolic rates of the resident microbial communities. We present here potential extracellular enzyme activities of leucine aminopeptidase (LAP) and alkaline phosphatase (AP) measured on basalt samples from different locations on Loihi Seamount, HI, coupled with analysis of prokaryotic biomass and pyrosequencing of the bacterial 16S rRNA gene. The community maximum potential enzyme activity (Vmax) of LAP ranged from 0.47 to 0.90 nmol (g rock)−1h−1; theVmaxfor AP was 28 to 60 nmol (g rock)−1h−1. TheKmof LAP ranged from 26 to 33 μM, while theKmfor AP was 2 to 7 μM. Bacterial communities on Loihi basalts were comprised primarily ofAlpha-,Delta-, andGammaproteobacteria,Bacteroidetes, andPlanctomycetes. The putative ability to produce LAP is evenly distributed across the most commonly detected bacterial orders, but the ability to produce AP is likely dominated by bacteria in the ordersXanthomonadales,Flavobacteriales, andPlanctomycetales. The enzyme activities on Loihi basalts were compared to those of other marine environments that have been studied and were found to be similar in magnitude to those from continental shelf sediments and orders of magnitude higher than any measured in the water column, demonstrating that the potential for exposed basalts to transform organic matter is substantial. We propose that microbial communities on basaltic rock play a significant, quantifiable role in benthic biogeochemical processes.

scholarly journals Distinct microbial composition and functions in an underground high-temperature hot spring at different depths

2019 ◽  
Author(s):  
Shijie Bai ◽  
Xiaotong Peng
Keyword(s):  
High Temperature ◽  
Microbial Communities ◽  
Hot Springs ◽  
Hot Spring ◽  
Hydrogen Oxidation ◽  
Archaeal Community ◽  
Limited Area ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Different Depths

Abstract. The microbial diversity and functions of three high-temperature neutral hot springs water samples at different depths (0 m, 19 m and 58 m) were investigated based on 16S rRNA gene sequencing and a functional gene array (GeoChip 5.0). The results revealed that the bacterial communities were distinct at different depths in the hot springs. Additionally, in response to the depths, bacterial/archaeal community compositions exhibited shifts over the depth profiles. Aquificae, Alpha-proteobacteria, and Deinococcus-Thermus were the dominating phyla at 0 m, 19 m, and 58 m, respectively. Hydrogenobacter, Sphingobium, and Thermus were the most abundant genera at 0 m, 19 m, and 58 m, respectively. The phylum Thaumarchaeota was the most abundant member of the archaeal community in the samples at different hot spring depths. Functional results of the microbial communities indicated that microbial metabolic functions were mainly related to sulfur, nitrogen cycling, and hydrogen oxidation. In summary, our results demonstrated that distinct microbial communities and functions were found at different depths of hot springs in a very limited area. These findings will provide new insights into the deep-subsurface biosphere associated with terrestrial hot springs.

scholarly journals Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Justinn Renelies-Hamilton ◽  
Kristjan Germer ◽  
David Sillam-Dussès ◽  
Kasun H. Bodawatta ◽  
Michael Poulsen
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Vertical Transmission ◽  
Priority Effects ◽  
Rrna Gene ◽  
Combined Effects ◽  
Microbial Composition ◽  
Host Fitness ◽  
Microbial Invasion ◽  
Host Taxon

ABSTRACT A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments. IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.

scholarly journals Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

2019 ◽  
Vol 7 (9) ◽  
pp. 357 ◽  
Author(s):  
Moonsuk Hur ◽  
Soo-Je Park
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Community Structure ◽  
16S Rrna ◽  
Microbial Communities ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Full Length ◽  
Rrna Gene ◽  
Microbial Composition

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

scholarly journals Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

2021 ◽  
Author(s):  
Patrick H. Thieringer ◽  
Alexander S. Honeyman ◽  
John R. Spear
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Surface Hydrology ◽  
Microbial Composition ◽  
16S Rrna Gene Analysis ◽  
High Concentrations ◽  
Recharge Rates

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular biological and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (~150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments.

scholarly journals Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

2019 ◽  
Author(s):  
Philipp Rausch ◽  
Malte Rühlemann ◽  
Britt Hermes ◽  
Shauni Doms ◽  
Tal Dagan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Evolutionary Patterns ◽  
Wide Range ◽  
Taxonomic Groups ◽  
And Function

AbstractBackgroundThe interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These interdependencies inspired a new view of multicellular organisms as “metaorganisms”. The goal of the Collaborative Research Center “Origin and Function of Metaorganisms” is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.MethodsIn order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon- and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.ConclusionWhile 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods and that metagenomic shotgun results are largely dependent on the employed pipeline. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

scholarly journals Dynamics and Heterogeneity of Microbial Communities in Urban Water Environments

2020 ◽  
Author(s):  
Yanqing Lian ◽  
Lisha Zhen ◽  
Xi Chen ◽  
Yang Li ◽  
Xiaona Li
Keyword(s):  
Microbial Communities ◽  
Urban Areas ◽  
Pathogenic Bacteria ◽  
Temporal Dynamics ◽  
Statistical Analyses ◽  
Polluted Water ◽  
Outer Side ◽  
Rrna Gene ◽  
The City ◽  
The 16S Rrna Gene

Abstract Water samples for the 16S rRNA gene and water quality analyses were collected from around 155 kilometers of river segments surrounding the urban areas in Xi’an of China. Multiple statistical analyses showed the temporal dynamics of microbial communities and heterogeneity in their spatial distributions. The dynamic shifts of microbial communities in the Chan, Ba, and Feng Rivers from the Spring to the Summer seasons were apparent, but little in the Zao River. The heterogeneity of microbial distributions was more due to the influence of hydrologic conditions and various sources of inflows in the rivers. The LEfSe analysis showed the Chan and Zao Rivers, both were more impacted by the sewage effluents, were more differentially abundant with bacteria related to polluted water, but the Ba and Feng Rivers, both on the outer side of the city, were more abundant with microbial communities in soil and freshwater environments in August. Multiple statistical analyses indicated that environmental variables had a significant impact on microbial communities. The GIS-based spatial analysis not only showed heterogeneity of microbial community distributions along the rivers, more importantly, could help identify locations where pathogenic bacteria presented.

Bushfire impacts on a threatened swamp ecosystem: responses of the soil microbial communities and restoration

2021 ◽  
Author(s):  
Nathali Machado de Lima ◽  
Alexandria Thomsen ◽  
Mark Ooi ◽  
Miriam Muñoz-Rojas
Keyword(s):  
Microbial Communities ◽  
Longwall Mining ◽  
Soil Microbial Communities ◽  
Environmental Indicators ◽  
Fire Season ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Drought Period ◽  
Soil Microbial ◽  
The Impact

&lt;p&gt;Australia faced the most extreme and prolonged fire season in 2019-2020, resulting in tragic habitat loss for many threatened species and the destruction of many ecological communities. &amp;#160;Newnes Plateau Shrub Swamps are peatlands located in the upper Blue Mountains region of New South Wales, Australia. These ecosystems perform many important ecological functions while absorbing and filtering water and releasing it slowly back to the environment. Their functions are related to the control of peak flow events, water purification and the harboring of many threatened plant and animal species. Despite their ecological importance, the area has been intensively degraded through longwall mining processes, resulting in the lowering and loss of water tables in the area. In December 2019 these impacts were compounded by an intense prolonged drought period and extensive wildfire. While the effects of these combined factors on the vegetation have been analysed and revealed remarkable negative impacts in the swamps under mining pressures, the effects on the soil microbial communities and related soil functions have not yet been studied. To investigate both drivers (fire and mining activities), we selected three mined swamps and three unmined swamps to assess their soil microbial composition and diversity through Next Generation Sequencing, and to characterise the soil chemical composition. At each site, we collected samples considering three treatments, one in the swamp valley fill and two at two different heights of the swamp valley margin, focusing on the soil close to specific groups of plants (e.g. sedges and shrubs). For each site and treatment, three soil samples (~ 10 m from each other) of 10x10 cm and ~ 3 to 5 cm of depth were collected using a trowel. We aim to build 16S rRNA gene libraries and co-relate them with the soil chemical variables, to assess the impact on these microbial communities and their possible use as environmental indicators and basis for future applied initiatives in conservation and restoration.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;

scholarly journals Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients

2016 ◽  
Vol 82 (22) ◽  
pp. 6633-6644 ◽  
Author(s):  
Francesco Paroni Sterbini ◽  
Alessandra Palladini ◽  
Luca Masucci ◽  
Carlo Vittorio Cannistraci ◽  
Roberta Pastorino ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Proton Pump Inhibitors ◽  
Proton Pump ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Content Type ◽  
Treatment Regimens ◽  
H Pylori ◽  
Content Status ◽  
Gastric Microbiota

ABSTRACTBesides being part of anti-Helicobacter pyloritreatment regimens, proton pump inhibitors (PPIs) are increasingly being used to treat dyspepsia. However, little is known about the effects of PPIs on the human gastric microbiota, especially those related toH. pyloriinfection. The goal of this study was to characterize the stomach microbial communities in patients with dyspepsia and to investigate their relationships with PPI use andH. pyloristatus. Using 16S rRNA gene pyrosequencing, we analyzed the mucosa-associated microbial populations of 24 patients, of whom 12 were treated with the PPI omeprazole and 9 (5 treated and 4 untreated) were positive forH. pyloriinfection. TheProteobacteria,Firmicutes,Bacteroidetes,Fusobacteria, andActinobacteriaphyla accounted for 98% of all of the sequences, withHelicobacter,Streptococcus, andPrevotellaranking among the 10 most abundant genera.H. pyloriinfection or PPI treatment did not significantly influence gastric microbial species composition in dyspeptic patients. Principal-coordinate analysis of weighted UniFrac distances in these communities revealed clear but significant separation according toH. pyloristatus only. However, in PPI-treated patients,Firmicutes, particularlyStreptococcaceae, were significantly increased in relative abundance compared to those in untreated patients. Consistently,Streptococcuswas also found to significantly increase in relation to PPI treatment, and this increase seemed to occur independently ofH. pyloriinfection. Our results suggest thatStreptococcusmay be a key indicator of PPI-induced gastric microbial composition changes in dyspeptic patients. Whether the gastric microbiota alteration contributes to dyspepsia needs further investigation.IMPORTANCEAlthough PPIs have become a popular treatment choice, a growing number of dyspeptic patients may be treated unnecessarily. We found that patients treated with omeprazole showed gastric microbial communities that were different from those of untreated patients. These differences regarded the abundances of specific taxa. By understanding the relationships between PPIs and members of the gastric microbiota, it will be possible to envisage new strategies for better managing patients with dyspepsia.

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