scholarly journals Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes

2021 ◽  
Vol 12 ◽  
Author(s):  
Qi Yan ◽  
Jianming Deng ◽  
Feng Wang ◽  
Yongqin Liu ◽  
Keshao Liu
Keyword(s):  
Community Assembly ◽  
454 Sequencing ◽  
Species Traits ◽  
Rrna Gene ◽  
Natural Environments ◽  
Ecological Processes ◽  
The Core ◽  
Core Species ◽  
Occurrence Patterns ◽  
Satellite Species

Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.

scholarly journals Can functional traits explain phylogenetic signal in the composition of a plant community?

2015 ◽  
Author(s):  
Daijiang Li ◽  
Anthoy R Ives ◽  
Donald M Waller
Keyword(s):  
Functional Traits ◽  
Community Assembly ◽  
Phylogenetic Signal ◽  
Species Traits ◽  
Functional Trait ◽  
Phylogenetic Information ◽  
Ecological Processes ◽  
Forest Sites ◽  
Species Abundances ◽  
Understory Plant

Phylogeny-based and functional trait-based analyses are two principle ways to study community assembly and underlying ecological processes. In principle, knowing all information about species traits would make phylogenetic information redundant, at least that component of phylogenetic signal in the distribution of species among communities that is caused by phylogenetically related species sharing similar traits. In reality, phylogenies may contain more information than a set of singular, discretely measured traits because we cannot measure all species traits and may misjudge which are most important. The extent to which functional trait information makes phylogenetic information redundant, however, has not been explicitly studied with empirical data in community ecology. Here, we use phylogenetic linear mixed models to analyze community assembly of 55 understory plant species in 30 forest sites in central Wisconsin. These communities show strong phylogenetic attraction, yet variation among sites in 20 environmental variables could not account for this pattern. Most of the 15 functional traits we measured had strong phylogenetic signal, but only three varied strongly among sites in ways that affected species' abundances. These three traits explained only 19% of variation in phylogenetic patterns of species co-occurrence. Thus, phylogenies appear to provide considerably more information about community assembly than the functional traits measured in this study, demonstrating the value of phylogeny in studying of community assembly processes even with abundant functional traits.

scholarly journals Putative functions and co-occurrence patterns of the microbial communities in natural and engineered ecosystems

2021 ◽  
Author(s):  
Yu Xia ◽  
Na Li ◽  
Yiyun Chen ◽  
Weijia Li ◽  
Xuwen He ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Rrna Gene ◽  
Natural Environments ◽  
Anaerobic Digesters ◽  
Network Analyses ◽  
Wb Network ◽  
Almost All ◽  
Occurrence Patterns

Abstract Understanding functions and co-occurrence patterns of microbial communities in various ecosystems enriches the knowledge on ecosystem characteristics and microbial ecology. However, such analyses have rarely been reported. Herein, functions and inter-taxa correlations of microbial communities in a set of natural environments (farmland (SA), forest soil (SB) and Caspian Sea sediments (CSS)) and engineered ecosystems (wastewater treatment plants (FW, WA and WB) and anaerobic digesters (AD)) were studied based on FAPROTAX and network analyses, respectively, by a collection of 115 samples from seven published 16S rRNA gene datasets generated by high-throughput sequencing. The results show that chemoheterotrophy related populations were the most abundant in almost all the communities. Their relative abundances (RAs) in the AD systems were the highest (43.7%±4.2%), followed by those of the soil environments (40.2%±1.9% in SA and 36.4%±2.0% in SB). For each ecosystem, the indicative community and overall community showed differentiations in several function categories. For example, the SA and SB indicative communities showed higher RAs in aerobic chemoheterotrophy, the CSS indicative community showed higher RAs in sulfate respiration, the AD indicative community showed higher RAs in fermentation, and the WB indicative community included higher RAs of predatory/exoparasitic bacteria. Three molecular ecological networks of the communities from the AD, WB and SB datasets were constructed, respectively. The WB network showed the highest proportion of negative correlations (70.4%), possibly attributed to the environmental pressure which aggravated microbial competition. The positively correlated taxa showed lower phylogenetic distances than the negatively correlated taxa on average in each network.

Intestinal helminths of lesser scaup ducks: patterns of association

1986 ◽  
Vol 64 (1) ◽  
pp. 132-141 ◽  
Author(s):  
Albert O. Bush ◽  
John C. Holmes
Keyword(s):  
Differential Susceptibility ◽  
The Other ◽  
Intestinal Helminths ◽  
Gammarus Lacustris ◽  
The Core ◽  
Core Species ◽  
Lesser Scaup ◽  
Associated Species ◽  
Satellite Species ◽  
Basic Similarity

The helminth communities of the small intestines of 45 lesser scaup ducks sampled from 13 lakes in Alberta, Canada, were examined for patterns of association among species. A core of eight frequent, numerous, and positively associated species provided a basic similarity across all host individuals. Six of these core species are specialists in lesser scaup, and the other two are generalists in waterfowl. A group of eight moderately frequent and numerous species, which were positively associated with the core species but not with each other, also contributed to this similarity; these secondary species included two specialists in scaup and three generalists in waterfowl. The 36 remaining "satellite species" appeared to be distributed randomly among birds. Variations among communities in individual birds were due largely to (i) differences in the numbers of two suites of helminth species, one using Hyalella azteca and the other Gammarus lacustris as intermediate host; (ii) differences in the numbers of the Hyalella suite, and in the presence or absence of some secondary or satellite species, associated with the lake from which the duck was taken; and (iii) differences in the total numbers of helminths per duck, which may be associated with differential susceptibility of individual ducks.

scholarly journals Disentangling Archaeal and Bacterial Biogeography and Co-occurrence Networks in Subtropical Mangrove Sediments Under Spartina Alterniflora Invasion

2020 ◽  
Author(s):  
Weidong Chen ◽  
Donghui Wen
Keyword(s):  
Spartina Alterniflora ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Mangrove Ecosystem ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Relative Role ◽  
Ecological Processes ◽  
Rare Taxa ◽  
Occurrence Patterns

Abstract Background: Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora invasion in China. Large knowledge gaps remain with regard to archaeal and bacterial communities assembly processes and microbial interactions under S. alterniflora invasion. Here, using 16S rRNA gene amplicon sequencing, we investigated the assembly processes and co-occurrence relationships of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China.Results: We found that the overall archaeal and bacterial communities were driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analysis showed that the network structure of bacteria was more complex than that of the archaea. Putative keystone taxa often had low relative abundances (conditionally rare taxa), suggesting conditionally rare taxa or low abundances taxa may significantly contribute to network stability. Moreover, we found that S. alterniflora invasion changed the microbial communities assembly and co-occurrence patterns, indicating that S. alterniflora affected the composition and stability of the microbial community.Conclusions: This study provides the first comparison in the biogeography and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem. And this is the first exploration about the effect of S. alterniflora invasion on archaeal and bacterial ecological processes and co-occurrence patterns. Our study considers that the control of S. alterniflora invasion is important for mangrove ecosystem function and service.

scholarly journals Community Assembly Mechanisms Underlying the Core and Random Bacterioplankton and Microeukaryotes in a River–Reservoir System

Water ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1127 ◽  
Author(s):  
Alain Isabwe ◽  
Kexin Ren ◽  
Yongming Wang ◽  
Feng Peng ◽  
Huihuang Chen ◽  
...  
Keyword(s):  
Community Assembly ◽  
Anthropogenic Impacts ◽  
Null Model ◽  
Distribution Patterns ◽  
Ecological Processes ◽  
The Core ◽  
Reservoir System ◽  
Environmental Selection ◽  
River Reservoir ◽  
Plankton Communities

Whether bacterioplankton are assembled in the same way as microeukaryotes is a key question that has been answered only partially in microbial ecology. In particular, relating distribution patterns to the underlying ecological processes for plankton communities in highly dynamic ecosystems, such as river–reservoirs subjected to anthropogenic impacts, remains largely unstudied. Here, we analyzed taxonomic distribution patterns, and unraveled community assembly processes underlying the core and random bacterioplankton and microeukaryotes from a subtropical river–reservoir system. These plankton domains were modelled using the spatial abundance distributions (SpADs) of the operational taxonomic units (OTUs) as a proxy for abundant and rare taxa delineation. Both bacterioplankton and microeukaryote plankton communities exhibited significant distance–decay relationships, and samples were grouped depending on reservoir or river habitats. The neutral community model showed that 35–45% of the plankton community variation could be explained by neutral processes. The phylogenetic null model revealed that dispersal limitation accounted for the largest percentage of pairwise comparisons (42–68%), followed by environmental selection (18–25%). We concluded that similar prevalence of ecological processes acting on particular subsets of the bacterioplankton and microeukaryotes might have resulted from similar responses to environmental change, potentially induced by human activities in the watershed.

scholarly journals Stochastic processes dominate community assembly in cichlid communities in Lake Tanganyika

2016 ◽  
Author(s):  
Thijs Janzen ◽  
Adriana Alzate ◽  
Moritz Muschick ◽  
Fons van der Plas ◽  
Rampal S. Etienne
Keyword(s):  
Stochastic Processes ◽  
Community Assembly ◽  
Environmental Conditions ◽  
Lake Tanganyika ◽  
Environmental Gradients ◽  
Cichlid Fish ◽  
Species Traits ◽  
Ecological Processes ◽  
African Great Lakes ◽  
Community Dissimilarity

ABSTRACTThe African Great Lakes are characterized by an extraordinary diversity of endemic cichlid fish species. The cause of this diversity is still largely unknown. Most studies have tried to solve this question by focusing on macro-evolutionary processes, such as speciation. However, the ecological processes determining local cichlid diversity have so far been understudied, even though knowledge on these might be crucial for understanding larger scale biodiversity patterns.Using trait, environmental and abundance data of cichlid fishes along 36 transects, we have studied how differences in local environmental conditions influence cichlid community assembly in the littoral of Lake Tanganyika, Zambia. We investigated changes in average trait values and in trait-based community assembly processes along three key environmental gradients.Species diversity and local abundance decreased with increasing sand cover and diet-associated traits changed with depth. Analyses on within-community trait diversity patterns indicated that cichlid community assembly was mainly driven by stochastic processes, to a smaller extent by processes that limit the similarity among co-existing species and least by filtering processes that limit the range of species traits occurring in an environment. Despite, the low impact of habitat filtering processes, we find community dissimilarity to increase with increasing environmental difference.Our results suggest that local environmental conditions determine cichlid abundance, while the predominance of stochastic community assembly across all environments explains why the communities with the highest abundances contain most species.

scholarly journals Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Zhiyuan Yao ◽  
Shicong Du ◽  
Chunling Liang ◽  
Yueji Zhao ◽  
Francisco Dini-Andreote ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Assembly ◽  
Salt Marshes ◽  
Bacterial Communities ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Gradient System ◽  
High Marsh ◽  
Ecological Processes ◽  
Topological Features

ABSTRACTBacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCESalt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.

Common and rare trout parasites in a small landscape system

Parasitology ◽  
1993 ◽  
Vol 106 (1) ◽  
pp. 101-105 ◽  
Author(s):  
R. Hartvigsen ◽  
O. Halvorsen
Keyword(s):  
Salmo Salar ◽  
Carrying Capacity ◽  
Salmo Trutta ◽  
Rescue Effect ◽  
The Core ◽  
Core Species ◽  
Landscape System ◽  
Colonization Ability ◽  
Effect Hypothesis ◽  
Satellite Species

SUMMARYBrown trout (Salmo trutta) from four lakes within an area of approximately 40 km2 were found to harbour nine helminth species. Crepidostomum metoecus could be classified as core species, while Crepidostomum farionis had an intermediate position. All the others could be classified as satellite species. Salmon (Salmo salar) fingerlings were grown to smolts in an earthpond over the summer. The fingerlings became infected with Crepidostomum spp. which may indicate a superior colonization ability in the core species. The results support the ‘rescue effect hypothesis’ rather than the ‘carrying capacity hypothesis’.

scholarly journals Disentangling archaeal and bacterial biogeography and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion

2020 ◽  
Author(s):  
Weidong Chen ◽  
Donghui Wen
Keyword(s):  
Spartina Alterniflora ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Mangrove Ecosystem ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Relative Role ◽  
Ecological Processes ◽  
Rare Taxa ◽  
Occurrence Patterns

Abstract Background Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora invasion in China. Large knowledge gaps remain with regard to archaeal and bacterial communities assembly processes and microbial interactions under S. alterniflora invasion. Here, using 16S rRNA gene amplicon sequencing, we investigated the assembly processes and co-occurrence relationships of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China.Results We found that the overall archaeal and bacterial communities were driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analysis showed that the network structure of bacteria was more complex than that of the archaea. Putative keystone taxa often had low relative abundances (conditionally rare taxa), suggesting conditionally rare taxa or low abundances taxa may significantly contribute to network stability. Moreover, we found that S. alterniflora invasion changed the microbial communities assembly and co-occurrence patterns, indicating that S. alterniflora affected the composition and stability of the microbial community.Conclusions This study provides the first comparison in the biogeography and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem. And this is the first exploration about the effect of S. alterniflora invasion on archaeal and bacterial ecological processes and co-occurrence patterns. Our study considers that the control of S. alterniflora invasion is important for mangrove ecosystem function and service.

scholarly journals Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

2021 ◽  
Author(s):  
Qiang Lin ◽  
Francisco Dini-Andreote ◽  
Travis B Meador ◽  
Roey Angel ◽  
Lenka Meszarosov ◽  
...  
Keyword(s):  
Microbial Community ◽  
Resource Availability ◽  
Community Assembly ◽  
Ecological Succession ◽  
Fungal Communities ◽  
Ecological Processes ◽  
Soil Age ◽  
Successional Stages ◽  
Occurrence Patterns ◽  
Microbial Community Assembly

Development of soil microbial communities along ecological succession is crucial for ecosystem functioning and maintenance. However, ecological processes mediating microbial community assembly and microbial co-occurrence patterns along ecological succession remain unclear. Here, we explored community phylogenetic structures, ecological processes driving community phylogenetic turnover, and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing prior studies of microbial phylogeny in community assembly, we proposed two conceptual models to better explain our results. At early successional stages, the significantly increasing phylogenetic clustering of bacterial communities with soil age was co-determined by the environmental selection from soil vegetation cover and by bacterial heterogeneous responses that less phylogenetically similar bacteria differently expanded their population in response to the increasing resource availability in soil along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community structure turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of the phylogeny between co-occurring fungi. This study provides new sights into ecological processes and mechanisms underlying bacterial and fungal community dynamics along ecological succession, thereby boosting our understanding of the interactions between microbial community assembly and soil environment gradients.

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