scholarly journals Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jie Yang ◽  
Yanfen Wang ◽  
Xiaoyong Cui ◽  
Kai Xue ◽  
Yiming Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Habitat Preferences ◽  
Biotic Interactions ◽  
Illumina Miseq ◽  
Detailed Comparison ◽  
Niche Differentiation ◽  
Species Selection ◽  
Biogeographic Patterns ◽  
Xilingol Grassland ◽  
Steppe Grassland

AbstractThe spatial variability of microorganisms in grasslands can provide important insights regarding the biogeographic patterns of microbial communities. However, information regarding the degree of overlap and partitions of microbial communities across different habitats in grasslands is limited. This study investigated the microbial communities in three distinct habitats from Xilingol steppe grassland, i.e. animal excrement, phyllosphere, and soil samples, by Illumina MiSeq sequencing. All microbial community structures, i.e. for bacteria, archaea, and fungi, were significantly distinguished according to habitat. A high number of unique microorganisms but few coexisting microorganisms were detected, suggesting that the structure of microbial communities was mainly regulated by species selection and niche differentiation. However, the sequences of those limited coexisting microorganisms among the three different habitats accounted for over 60% of the total sequences, indicating their ability to adapt to variable environments. In addition, the biotic interactions among microorganisms based on a co-occurrence network analysis highlighted the importance of Microvirga, Blastococcus, RB41, Nitrospira, and four norank members of bacteria in connecting the different microbiomes. Collectively, the microbial communities in the Xilingol steppe grassland presented strong habitat preferences with a certain degree of dispersal and colonization potential to new habitats along the animal excrement- phyllosphere-soil gradient. This study provides the first detailed comparison of microbial communities in different habitats in a single grassland, and offers new insights into the biogeographic patterns of the microbial assemblages in grasslands.

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

Temperature as a Proximate Factor in Orientation Behavior

1977 ◽  
Vol 34 (5) ◽  
pp. 734-739 ◽  
Author(s):  
William W. Reynolds
Keyword(s):  
Temperature Response ◽  
Biotic Interactions ◽  
Niche Differentiation ◽  
Behavioral Thermoregulation ◽  
Size Segregation ◽  
Ecological Value ◽  
Thermal Requirements ◽  
Prey Location ◽  
Proximate Factor ◽  
Species Specific

Temperature serves as a proximate factor (cue, guidepost, sign stimulus, or directive factor) affecting locomotor responses of fishes. Although temperature can also serve as an ultimate ecological factor, as in behavioral thermoregulation, nonthermal factors may in some cases provide the ultimate adaptive or ecological value of a temperature response; some examples are habitat selection, intraspecific size segregation, interspecific niche differentiation, isolating mechanisms, predator avoidance, prey location, escape reactions, and migrations (thermoperiodic, diel, seasonal, spawning). Conversely, nonthermal variables such as light intensity or water depth may act as accessory proximate factors in thermoregulation. In spawning migrations, thermal requirements of eggs and larvae may take precedence over the (often different) preferenda or optima of adults. Although thermal responses of fishes are largely innate and species specific, ontogenetic and other changes can occur. Since temperature can serve as an unconditioned reinforcer in operant conditioning, thermal responses are not limited to simple kineses or taxes. Nonthermal factors such as photoperiod, circadian rhythms, currents, social and biotic interactions, stresses, infections, or chemicals can affect thermal responses, and may account for some lack of conformity between laboratory preferenda and field distributions and behaviors. Key words: thermoregulation, orientation, preferendum, selection, preference, avoidance, behavior, temperature, fish, responses

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

scholarly journals Agricultural constraints on microbial resource use and niche breadth in drainage ditches

2017 ◽  
Author(s):  
Ellard R Hunting ◽  
Henrik Barmentlo ◽  
Maarten Schrama ◽  
Peter van Bodegom ◽  
Yujia Zhai ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Resource Utilization ◽  
Agricultural Land ◽  
Niche Breadth ◽  
Niche Differentiation ◽  
Drainage Ditches ◽  
Substrate Quality ◽  
Degradation Rates ◽  
Natural Communities

Background. Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in organic matter (OM) degradation in natural systems remains poorly understood. Methods. Here we evaluated effects of differences in organic matter (OM) related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed 1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and 2) how changes in community resource niche breadth translates to the degradation of natural OM. Results. A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality. Discussion. Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.

Alleviating Continuous Monocropping Obstacle in Melon: Biological Elimination of Phenolic Acid

2020 ◽  
Author(s):  
Huiqin Xie ◽  
Yongli Ku ◽  
Xiangna Yang ◽  
Le Cao ◽  
Xueli Mei ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Phenolic Acids ◽  
Fruit Quality ◽  
High Performance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Continuous Cropping ◽  
Soil Microbial

Abstract Background: Melon (Cucumis melo L.) is one of the most important fruit crops grown in China. However, the yield and quality of melon have significantly declined under continuous cropping. Phenolic acids are believed to be associated with the continuous monocropping obstacle (CMO) and can influence plant microbe interactions. Coumaric acid (CA) is one of the major phenolic acids found in melon root exudates. The objectives of this study were to estimate the elimination of CA by the soil bacterium K3 as well as its effects on mitigating melon CMO. CA degradation was investigated by monitoring the CA retained in the growth medium using high performance liquid chromatography (HPLC). The effects of CA and K3 on rhizosphere soil microbial communities were investigated by the spread plate method and Illumina MiSeq sequencing. Furthermore, the effects of CA and K3 on melon seedling growth were measured under potted conditions. The changes in soil enzymes and fruit quality under K3 amendment were examined in a greenhouse experiment. Result:The results suggest that the addition of CA had the same result as the CMO, such as deterioration of the microbial community and slower growth of melon plants. HPLC and microbial analysis showed that K3 had a pronounced ability to decompose CA and could improve the soil microbial community environment. Soil inoculation with K3 agent could significantly improve the fruit quality of melon.Conclusion: Our results show that the effects of K3 in the soil are reflected by changes in populations and diversity of soil microbes and suggest that deterioration of microbial communities in soil might be associated with the growth constraint of melon in continuous monoculture systems.

scholarly journals The largest known cowrie and the iterative evolution of giant cypraeid gastropods

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Stefano Dominici ◽  
Mariagabriella Fornasiero ◽  
Luca Giusberti
Keyword(s):  
Species Richness ◽  
Evolutionary History ◽  
Western Europe ◽  
Negative Relationship ◽  
Species Selection ◽  
Biogeographic Patterns ◽  
Large Size ◽  
Northeastern Italy ◽  
History Of ◽  
Iterative Evolution

AbstractBased on the fossil record, we explore the macroevolutionary relationship between species richness and gigantism in cowries (Cypraeidae), the best-studied family of gastropods, with a global diversity distribution that parallels that of tropical corals, mangroves and seagrasses. We introduce Vicetia bizzottoi sp. nov. based on a Priabonian fossil found in northeastern Italy, the largest documented cowrie found so far and the youngest of a lineage of Eocene Gisortiinae species. The Gisortiinae stratigraphic record in western Europe indicates that species selection favoured large size and armouring of the shell. Palaeoecology and per-stage species richness suggest that gigantism occurred in peripheral habitats with respect to diversity hotspots, where smaller species were favoured. The Eocene–Oligocene boundary was marked by a turnover and the Chattian global warming favoured small-sized species of derived clades. Species selection leading to gigantism is further documented in Miocene lineages of Zoila and Umbilia, in the southern hemisphere, two extant genera distributed at the periphery of modern diversity hotspots, suggesting that the negative relationship between size and diversity is a recurring pattern in the evolutionary history of cowries. This palaeontological evidence is projected onto the existing hypotheses that explain analogous biogeographic patterns in various other taxa. Likewise, body size-species richness negative relationship was possibly driven in cowries by physiological, ecological and life history constraints.

scholarly journals Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities

2020 ◽  
Vol 287 (1927) ◽  
pp. 20192945 ◽  
Author(s):  
Cristina M. Herren
Keyword(s):  
Microbial Communities ◽  
Biotic Interactions ◽  
Invasion Risk ◽  
Invasional Meltdown ◽  
Native Community ◽  
Exchange Networks ◽  
Composition And Structure ◽  
Metabolite Exchange ◽  
Successful Invader ◽  
The Impact

The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this ‘critical’ level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.

scholarly journals Effects of a chemical additive on the fermentation, microbial communities, and aerobic stability of corn silage with or without air stress during storage

2020 ◽  
Vol 98 (8) ◽  
Author(s):  
Érica B da Silva ◽  
Rebecca M Savage ◽  
Amy S Biddle ◽  
Stephanie A Polukis ◽  
Megan L Smith ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Storage Period ◽  
Illumina Miseq ◽  
Corn Silage ◽  
Potassium Sorbate ◽  
Chemical Additive ◽  
Pichia Kudriavzevii ◽  
Aerobic Stability ◽  
Whole Plant ◽  
Fermentation Profile

Abstract We evaluated the effects of a chemical additive on the microbial communities, fermentation profile, and aerobic stability of whole-plant corn silage with or without air stress during storage. Whole-plant corn was either untreated or treated with a chemical additive containing sodium benzoate, potassium sorbate, and sodium nitrite at 2 or 3 liters/t of fresh forage weight. Ten individually treated and replicated silos (7.5 liters) were made for each treatment. Half of the silos remained sealed throughout a 63-d storage period, and the other half was subjected to air stress for 2 h/wk. The composition of the bacterial and fungal communities of fresh forage and silages untreated or treated with 2 liters/t of fresh forage weight was analyzed by Illumina Miseq sequencing. Treated silage had greater (P < 0.05) aerobic stability than untreated, even when subjected to air stress during storage, but the numbers of yeasts culturable on selective agar were not affected. However, the additive reduced the relative abundance (RA) of the lactating-assimilating yeast Candida tropicalis (P < 0.01). In air-stressed silages, untreated silage had a greater (P < 0.05) RA of Pichia kudriavzevii (also a lactate assimilator) than treated silage, whereas treated silage was dominated by Candida humilis, which is usually unable to assimilate lactate or assimilates it slowly. The additive improved the aerobic stability by specifically preventing the dominance of yeast species that can consume lactate and initiate aerobic spoilage. To the best of our knowledge, this is the first work that identifies the specific action of this additive on shifting the microbial communities in corn silage.

scholarly journals The female urinary microbiota in relation to the reproductive tract microbiota

2019 ◽  
Author(s):  
Chen Chen ◽  
Lilan Hao ◽  
Weixia Wei ◽  
Fei Li ◽  
Liju Song ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Reproductive Tract ◽  
Chinese Women ◽  
Uterine Cavity ◽  
Detailed Comparison ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Urogenital System ◽  
Urinary Microbiota

AbstractHuman urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear.Here we collected the urine samples from 147 Chinese women of reproductive age, and explored the nature of colonization by 16S rRNA gene amplicon sequencing, real-time qPCR and live bacteria culture. To demonstrate utility intra-individual Spearman’s correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Types of diverse, Streptococcus-dominated, and Lactobacillus-dominated were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multi-sites of reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of vagina in the same women.Our data demonstrates the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.

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