Stochastic processes dominate marine free-living Vibrio community assembly in a subtropical gulf

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Nan Li ◽  
Ke Dong ◽  
Gonglingxia Jiang ◽  
Jinli Tang ◽  
Qiangsheng Xu ◽  
...  
Keyword(s):  
Stochastic Processes ◽  
Trophic State ◽  
Heterotrophic Bacteria ◽  
Variation Partitioning ◽  
Geographic Distance ◽  
Alpha Diversity ◽  
Mantel Test ◽  
Beibu Gulf ◽  
Assembly Features ◽  
Marine Environmental

ABSTRACT Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and assembly features of Vibrio, as well as their relationship with the environmental factors in the subtropical Beibu Gulf. We found that the alpha diversity of Vibrio increased in parallel with the trophic state they occupy. A Mantel test indicated that the trophic state was correlated to Vibrio beta diversity and the correlation gradually strengthened at higher trophic states. Variation partitioning analysis suggested that the geographic distance was an important factor impacting the variables of Vibrio communities in all the samples, but nutrients exerted more influence in the more highly eutrophic samples. Our results demonstrated that stochastic processes govern the turnover of marine Vibrio communities in the Beibu Gulf and that ecological drift was the most important process for assembly of the Vibrio communities.

Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Dan He ◽  
Lijuan Ren ◽  
Qinglong L Wu
Keyword(s):  
Stochastic Processes ◽  
Bacterial Communities ◽  
Taihu Lake ◽  
Submerged Macrophytes ◽  
Geographic Distance ◽  
Null Model ◽  
Alpha Diversity ◽  
Growing Season ◽  
Epiphytic Bacteria ◽  
Alpha And Beta Diversity

ABSTRACT Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes’ effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.

scholarly journals Geographic sharing of ribotype patterns in Enterococcus faecalis for bacterial source tracking

2007 ◽  
Vol 5 (4) ◽  
pp. 539-551 ◽  
Author(s):  
Peter G. Hartel ◽  
Robin L. Kuntz ◽  
Karen Rodgers ◽  
Samuel P. Myoda ◽  
Kerry J. Ritter ◽  
...  
Keyword(s):  
New York ◽  
Enterococcus Faecalis ◽  
Wastewater Treatment Plants ◽  
Geographic Distance ◽  
Similarity Index ◽  
Clonal Diversity ◽  
Mantel Test ◽  
Source Tracking ◽  
Tolerance Level ◽  
Bacterial Source Tracking

The limited host range of Enterococcus faecalis may reduce its clonal diversity and thereby increase its geographic sharing of ribotype patterns. Such sharing would be advantageous for bacterial source tracking (BST). We determined the geographic sharing of ribotype patterns in 752 Ent. faecalis isolates obtained primarily from wastewater treatment plants in Delaware (15 locations; 490 isolates), Georgia (2 locations; 48 isolates), Idaho (1 location; 118 isolates), New York (2 locations; 48 isolates), and Puerto Rico (2 locations; 48 isolates). Isolates were ribotyped with a RiboPrinter. When pooled across all locations and analyzed at a similarity index of 100% and a tolerance level of 1.00%, the 752 Ent. faecalis isolates yielded 652 different ribotypes, of which 429 (66%) were unshared. Even when the matching criterion was relaxed by decreasing the tolerance level from 1% to 10% or lowering the similarity cutoff from 100% to 90%, half or almost half of the ribotypes were unshared. A Mantel test of zero correlation showed no statistically significant correlation between ribotype patterns and geographic distance among the 32 samples (one location at one time) at either the 1.00% (P = 0.91) or 10.00% (P = 0.83) tolerance levels. Therefore, the percentage of ribotype patterns shared between two locations did not increase as the distance between locations decreased. In the case of BST, a permanent host origin database sufficiently large to encompass these ribotype patterns would be time-consuming and expensive to construct.

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

Environmental correlates of herpetofaunal diversity in Costa Rica

2010 ◽  
Vol 26 (5) ◽  
pp. 521-531 ◽  
Author(s):  
David Laurencio ◽  
Lee A. Fitzgerald
Keyword(s):  
Costa Rica ◽  
Species Diversity ◽  
Beta Diversity ◽  
Geographic Distance ◽  
Alpha Diversity ◽  
High Elevation ◽  
Diversity Patterns ◽  
Regional Diversity ◽  
Environmental Correlates ◽  
High Elevation Site

Abstract:Disentangling local and historical factors that determine species diversity patterns at multiple spatial scales is fundamental to elucidating processes that govern ecological communities. Here we investigated how environmental correlates may influence diversity at local and regional scales. Primarily utilizing published species lists, amphibian and reptile alpha and beta diversity were assessed at 17 well-surveyed sites distributed among ecoregions throughout Costa Rica. The degree to which regional species diversity patterns were related to environmental variables and geographic distance was determined using Canonical Correspondence Analysis and Mantel tests. Amphibian alpha diversity was highest in lowland Pacific sites (mean = 43.3 species) and lowest at the high elevation site (9 species). Reptile alpha diversity values were high for both lowland Atlantic (mean = 69.5 species) and lowland Pacific (mean = 67 species) sites and lowest for the high elevation site (8 species). We found high species turnover between local sites and ecoregions, demonstrating the importance of beta diversity in the determination of regional diversity. For both amphibians and reptiles, beta diversity was highest between the high-elevation site and all others, and lowest among lowland sites within the same ecoregion. The effect of geographic distance on beta diversity was minor. Ecologically significant climatic variables related to rain, temperature, sunshine and insolation were found to be important determinants of local and regional diversity for both amphibians and reptiles in Costa Rica.

scholarly journals The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

2015 ◽  
Author(s):  
Chuck Pepe-Ranney ◽  
Ed Hall
Keyword(s):  
Heterotrophic Bacteria ◽  
Alpha Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Competitive Balance ◽  
Community Membership ◽  
Resource Space ◽  
Plankton Communities ◽  
Planktonic Communities

The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm versus planktonic) has a stronger influence on community composition.

scholarly journals Low Divergence Among Natural Populations of Cornus kousa subsp. chinensis Revealed by ISSR Markers

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1082 ◽  
Author(s):  
Jia-Qiu Yuan ◽  
Qin Fang ◽  
Guo-Hua Liu ◽  
Xiang-Xiang Fu
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
In Situ Conservation ◽  
Geographic Distance ◽  
Natural Populations ◽  
Issr Markers ◽  
Mantel Test ◽  
Distribution Area ◽  
Genetic Characteristics ◽  
Cornus Kousa

Research Highlights: Taking Chinese dogwood (Cornus kousa subsp. chinensis) as an example, the genetic characteristics of natural populations collected from main a distribution area were evaluated using intersimple sequence repeat (ISSR) markers to reveal the genetic basis for further selection and breeding. Background and Objectives: Chinese dogwood is a small understory tree that is widely distributed in China. Chinese dogwood has attracted interest for its potential horticultural and ornamental values, and its natural resource potential urgently needs to be estimated. Materials and Methods: In this study, the genetic diversity of 12 natural populations collected from six provinces containing 223 individuals was evaluated based on ISSR markers. Results: Relatively high levels of genetic diversity were found at both the population and individual levels. The Shannon’s diversity index (I) among individuals (0.504) was higher than that among populations (0.338). Analysis of molecular variance (AMOVA) revealed that genetic variation mainly existed within populations (61.55%) rather than among populations (38.45%). According to the STRUCTURE analysis, 12 populations were assigned to two groups, i.e., the northern and southern ecological regions, which are separated by the Yangtze River. A Mantel test analysis showed that there was no significant correlation between genetic distance and geographic distance. Conclusions: Considering the breeding system of dogwoods, we speculated that the genetic characteristics of the natural populations of this species would be affected by the dispersal mode of its pollens and seeds; additionally, genetic drift could play an important role in its genetic differentiation. In conclusion, in situ conservation is recommended for Chinese dogwood based on our results.

Genetic variability in Indian populations of banana corm weevil [Cosmopolites sordidus (Coleoptera: Curculionidae)] assessed by RAPDs and AFLPs

2017 ◽  
Vol 37 (03) ◽  
pp. 149-162 ◽  
Author(s):  
Sweta Kumari U. Yadav ◽  
Jyotsna Singh ◽  
B. Padmanaban ◽  
Lalitha Sunil Kumar
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Hot Spot ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Mantel Test ◽  
Cosmopolites Sordidus ◽  
Restricted Gene Flow ◽  
Control And Management ◽  
Economic Pest

AbstractCosmopolites sordidus(Germar), commonly known as banana corm weevil, is an important economic pest in Asia that can cause severe yield loss depending upon the stage at which infestation occurs. In spite of its economic importance, little is known about the population structure of this pest in India. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to characterize the population genetic structure ofC. sordiduscollected from five hot spot locations in India. Nineteen RAPD primers and five selective AFLP primer combinations generated 147 and 304 amplification products, respectively. UPGMA dendrograms generated with both marker systems failed to reveal populations clustered based on geographic distance, which was confirmed by the Mantel test, which did not show a strong correlation between genetic distance and geographic distance. Values of indices of genetic identity showed that the populations were closely related. Though the gene flow estimate (Nm) between the populations was 0.469, suggesting restricted gene flow, the populations are not genetically distinct. These observations suggest that the range expansion of this banana pest in India has taken place through transport of infested corms and plant material, resulting in genetically close populations that are geographically distinct. These results provide important information on the population structure of this pest in India, which will aid in designing suitable strategies for its control and management, especially with respect to insecticide resistance.

scholarly journals Phytoplankton alpha diversity indices response the trophic state variation in hydrologically connected aquatic habitats in the Harbin Section of the Songhua River

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fanhua Meng ◽  
Zhenxiang Li ◽  
Lei Li ◽  
Feng Lu ◽  
Yan Liu ◽  
...  
Keyword(s):  
Trophic State ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Freshwater Ecosystem ◽  
Hydrological Connectivity ◽  
Trophic State Index ◽  
Aquatic Habitats ◽  
Songhua River ◽  
State Variation ◽  
The Songhua River

AbstractThe relationship between biodiversity and ecological functioning is a central issue in freshwater ecology, but how this relationship is influenced by hydrological connectivity stress is still unknown. In this study we analyzed the dynamic of the phytoplankton alpha diversity indices and their relationships with trophic state in two hydrologically connected aquatic habitats (Jinhewan Wetland and Harbin Section of the Songhua River) in the Songhua River Basin in northeast China. We hypothesized that the phytoplankton alpha-diversity indices have the potential to provide a signal linking trophic state variation in hydrologically connected aquatic habitats. Our results showed the Cyanophyta and Bacillariophyta were abundant at most stations. T-test showed that phytoplankton alpha diversity indices varied significantly between rainy season and dry season. Trophic State Index recorded that a meso-trophic to eutrophic states of two connected habits during study period. Multivariate statistical analysis revealed that the dynamic of phytoplankton alpha diversity index was closely associated with trophic states change. Our result indicated that hydrological connectivity is a key factor influenced phytoplankton community assembly. In addition, it is beneficial to develop an integrated approach to appropriately describe and measure the trophic state variations of hydrologically connected aquatic habits in freshwater ecosystem.

scholarly journals Genetic variability of Conopophaga lineata (Conopophagidae) (Wied-Neuwied, 1831) in Atlantic Forest fragments

2007 ◽  
Vol 67 (4 suppl) ◽  
pp. 859-865 ◽  
Author(s):  
GPM. Dantas ◽  
FR. Santos ◽  
MA. Marini
Keyword(s):  
Genetic Variability ◽  
Forest Fragmentation ◽  
Atlantic Forest ◽  
Geographic Distance ◽  
Great Part ◽  
Mantel Test ◽  
Conservation Strategies ◽  
Forest Fragments ◽  
Genetic Population ◽  
Bird Populations

Forest fragmentation affects bird populations in many ways, modifying the composition of communities and favouring open country species. The Atlantic Forest is considered one of the most important biomes in the world, due to its great biodiversity, accelerated rates of deforestation, and high endemism. Despite these characteristics, few studies have evaluated the effects of forest fragmentation in the genetic structure of Atlantic forest bird populations. So, this study aims to verify the effects of forest fragmentation in the genetic population structure of Conopophaga lineata, through RAPD markers. To achieve this goal, 89 C. lineata individuals were captured in nine Atlantic Forest fragments in Minas Gerais State. The RAPD data indicate that forest fragmentation has not affected the genetic variation of C. lineata populations (Mann-Whitney U = 3.50; p = 0.11). Great part of the genetic variability of this species is found within populations and it was not observed a correlation between genetic and geographic distance (Mantel test t = 0.6250; p = 073). UPGMA analyses did not show defined clades and all branches showed low statistical support. The low population differentiation observed in this species can be due to a high gene flow among populations or a recent fragmentation. Thus, the current diversity status of C. lineata populations indicates that this species is not significantly affected by fragmentation. However, more genetic studies are essential to improve conservation strategies of Brazilian Atlantic Forest birds.

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