scholarly journals Below-ground plant–fungus network topology is not congruent with above-ground plant–animal network topology

2015 ◽  
Vol 1 (9) ◽  
pp. e1500291 ◽  
Author(s):  
Hirokazu Toju ◽  
Paulo R. Guimarães ◽  
Jens M. Olesen ◽  
John N. Thompson
Keyword(s):  
Network Topology ◽  
Network Architecture ◽  
Community Dynamics ◽  
Species Coexistence ◽  
Interspecific Interactions ◽  
Fungal Species ◽  
Sequencing Data ◽  
Phylogenetic Groups ◽  
Form Complex ◽  
Below Ground

In nature, plants and their pollinating and/or seed-dispersing animals form complex interaction networks. The commonly observed pattern of links between specialists and generalists in these networks has been predicted to promote species coexistence. Plants also build highly species-rich mutualistic networks below ground with root-associated fungi, and the structure of these plant–fungus networks may also affect terrestrial community processes. By compiling high-throughput DNA sequencing data sets of the symbiosis of plants and their root-associated fungi from three localities along a latitudinal gradient, we uncovered the entire network architecture of these interactions under contrasting environmental conditions. Each network included more than 30 plant species and hundreds of mycorrhizal and endophytic fungi belonging to diverse phylogenetic groups. The results were consistent with the notion that processes shaping host-plant specialization of fungal species generate a unique linkage pattern that strongly contrasts with the pattern of above-ground plant–partner networks. Specifically, plant–fungus networks lacked a “nested” architecture, which has been considered to promote species coexistence in plant–partner networks. Rather, the below-ground networks had a conspicuous “antinested” topology. Our findings lead to the working hypothesis that terrestrial plant community dynamics are likely determined by the balance between above-ground and below-ground webs of interspecific interactions.

scholarly journals New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

2021 ◽  
Vol 7 (3) ◽  
pp. 207
Author(s):  
Lene Lange ◽  
Kristian Barrett ◽  
Anne S. Meyer
Keyword(s):  
Fungal Species ◽  
Fungal Genome ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
New Approach ◽  
Fungal Enzyme ◽  
Biomass Processing ◽  
Fungal Genomes ◽  
Robust Prediction ◽  
Fungal Kingdom

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.

scholarly journals Topographic Effects on the Spatial Species Associations in Diverse Heterogeneous Tropical Evergreen Forests

2021 ◽  
Vol 13 (5) ◽  
pp. 2468
Author(s):  
Nguyen Hong Hai ◽  
Yousef Erfanifard ◽  
Van Bac Bui ◽  
Trinh Hien Mai ◽  
Any Mary Petritan ◽  
...  
Keyword(s):  
Species Interactions ◽  
Species Coexistence ◽  
Spatial Scales ◽  
Interspecific Interactions ◽  
Spatial Association ◽  
Topographic Effects ◽  
Habitat Association ◽  
Important Species ◽  
Evergreen Forests ◽  
Partial Overlap

Studying spatial patterns and habitat association of plant communities may provide understanding of the ecological mechanisms and processes that maintain species coexistence. To conduct assessments of correlation between community compositions and habitat association, we used data from two topographically different plots with 2 ha area in tropical evergreen forests with the variables recorded via grid systems of 10 × 10 m subplots in Northern-Central Vietnam. First, we tested the relationship between community composition and species diversity indices considering the topographical variables. We then assessed the interspecific interactions of 20 dominant plant species using the nearest-neighbor distribution function, Dij(r), and Ripley’s K-function, Kij(r). Based on the significant spatial association of species pairs, indices of interspecific interaction were calculated by the quantitative amounts of the summary statistics. The results showed that (i) community compositions were significantly influenced by the topographic variables and (ii) almost 50% significant pairs of species interactions were increased with increasing spatial scales up to 10–15 m, then declined and disappeared at scales of 30–40 m. Segregation and partial overlap were the dominant association types and disappeared at larger spatial scales. Spatial segregation, mixing, and partial overlap revealed the important species interactions in maintaining species coexistence under habitat heterogeneity in diverse forest communities.

Complex environments alter competitive dynamics in fungi

2021 ◽  
Author(s):  
Justin Chan ◽  
Stephen Bonser ◽  
Michael M. Kasumovic ◽  
Jeff Powell ◽  
William Kirkham Cornwell
Keyword(s):  
Interspecific Interactions ◽  
Fungal Species ◽  
Wood Block ◽  
Complex Environments ◽  
Biotic Factor ◽  
Pairwise Interactions ◽  
Agar Media ◽  
Contextual Environment ◽  
Natural Settings ◽  
Natural Communities

Competition is a key biotic factor that often structures natural communities. Many attempts to disentangle how competition shapes natural communities have relied on experiments on simplified systems or through simple mathematical models. But these simplified approaches are limited in their ability to represent the complexity seen in more natural settings. Here, we considered the competitive pairwise dynamics between four saprotrophic fungal species. We tested whether the contextual environment changed these dynamics, repeating competitive experiments in a simple agar media and a more ecologically realistic wood block setting. We found that the competitive outcomes on agar media differed from those within the wood blocks. While superior competitors were identified across all pairwise interactions on agar, within the wood blocks, two of six interactions resulted in deadlock, where neither competitor could breach territory of the other, and one interaction resulted in a reversed competitive outcome. These results suggest that the complexity within natural substrates can alter the strength of interspecific interactions and may contribute to coexistence and the resulting high diversity of fungi often observed within wood.

Foraging behaviour in East Asian desert rodents and its implications on coexistence

2016 ◽  
Vol 62 (3-4) ◽  
pp. 171-177 ◽  
Author(s):  
Ling-Ying Shuai ◽  
Yan-Ling Song ◽  
Burt P. Kotler ◽  
Keren Embar ◽  
Zhi-Gao Zeng
Keyword(s):  
Foraging Behaviour ◽  
Species Coexistence ◽  
Interspecific Interactions ◽  
Interference Competition ◽  
Foraging Efficiency ◽  
Gobi Desert ◽  
Patch Use ◽  
Desert Rodents ◽  
Daily Scale

We studied the foraging behaviour of two sympatric rodents (Meriones meridianus and Dipus sagitta) in the Gobi Desert, Northwestern China. The role of the foraging behaviour in promoting species coexistence was also examined. We used giving-up densities (GUDs) in artificial food patches to measure the patch use of rodents and video trapping to directly record the foraging behaviour, vigilance, and interspecific interactions. Three potential mechanisms of coexistence were evaluated (1) microhabitat partitioning; (2) spatial heterogeneity of resource abundance with a tradeoff in foraging efficiency vs. locomotion; and (3) temporal partitioning on a daily scale. Compared to M. meridianus, D. sagitta generally possessed lower GUDs, spent more time on patches, and conducted more visits per tray per capita, regardless of microhabitat. However, M. meridianus possessed advantages in average harvesting rates and direct interference against D. sagitta. Our results only partly support the third mechanism listed above. We propose another potential mechanism of coexistence: a tradeoff between interference competition and safety, with M. meridianus better at interference competition and D. sagitta better at avoiding predation risk. This mechanism is uncommon in previously studied desert rodent systems.

scholarly journals Links between mouse and vole social networks and their gut microbiomes support predictions from metacommunity theory

2020 ◽  
Author(s):  
Joël W. Jameson ◽  
Steven W. Kembel ◽  
Denis Réale
Keyword(s):  
Social Networks ◽  
Host Species ◽  
Community Dynamics ◽  
Peromyscus Maniculatus ◽  
Interspecific Interactions ◽  
Host Community ◽  
Social Proximity ◽  
Strongly Connected ◽  
Bacterial Transmission

ABSTRACTMetacommunity theory predicts that strongly connected individuals will harbour similar gut microbiomes (GMs) and affiliating with more individuals should increase GM diversity. Additionally, cross-species bacterial transmission may play a role in how interspecific interactions affect host community dynamics. We tracked sympatric mice (Peromyscus maniculatus) and voles (Myodes gapperi) and constructed social networks for each species and both species together. We tested whether: 1) similarity in GM composition between individuals correlates with their social proximity within and across species; 2) GM diversity correlates with a host’s number of conspecific or heterospecific neighbours. We could not differentiate associations between GM composition and mouse social proximity or habitat. In voles, social proximity explained part of the GM composition. GM composition associated with interspecific social proximity, and mouse GM diversity correlated with number of vole neighbours. Contributions of host-host bacterial transmission to the GM partly follow metacommunity theory but depend on host species.

scholarly journals Damming in the Madeira River modifies the food spectrum of piscivorous and affects their resource partitioning

2021 ◽  
Vol 19 (3) ◽  
Author(s):  
Alessandra Pasian Lonardoni ◽  
Cristhiana Paula Röpke ◽  
Taís Melo ◽  
Gislene Torrente-Vilara
Keyword(s):  
Resource Partitioning ◽  
Species Coexistence ◽  
Niche Breadth ◽  
Interspecific Interactions ◽  
Species Abundance ◽  
Hydroelectric Power Plant ◽  
Hydroelectric Power ◽  
Stomach Fullness ◽  
Congeneric Species ◽  
Madeira River

Abstract Phylogenetic proximity suggests some degree of diet similarity among species. Usually, studies of diet show that species coexistence is allowed by partitioning food resources. We evaluate how visually oriented piscivorous fishes (Characiformes) share prey before and after building the Santo Antônio Hydroelectric Power Plant (HPP) in the Madeira River (Brazil), the largest muddy-water tributary of the Amazon River. Piscivorous species (Acestrorhynchus falcirostris, Acestrorhynchus heterolepis, Hydrolycus scomberoides, and Rhaphiodon vulpinus) were sampled under pristine (pre-HPP) and disturbed (post-HPP) environmental conditions. We analyzed species abundance and stomach contents for stomach fullness and prey composition to check variations between congeneric and non-congeneric species. The percent volume of prey taxa was normalized by stomach fullness and grouped into the taxonomic family level to determine diet, niche breadth, and overlap. Only R. vulpinus abundance increased in post-HPP. There was no significant variation in niche breadth between the periods, while niche overlap decreased in congeneric and non-congeneric species. Our results indicate that river impoundment affected piscivorous fishes in distinct ways and modified their resource partitioning. Therefore, evaluate interspecific interactions is a required tool to understand how fishes respond to river damming.

Analysis of Issues in SDN Security and Solutions

2018 ◽  
pp. 217-239
Author(s):  
Ankur Dumka ◽  
Hardwari Lal Mandoria ◽  
Anushree Sah
Keyword(s):  
Network Topology ◽  
Network Architecture ◽  
Denial Of Service ◽  
Network Services ◽  
Software Defined Network ◽  
Denial Of Service Attack ◽  
Man In The Middle ◽  
Service Attack ◽  
Topology Information ◽  
The Given

The chapter surveys the analysis of all the security aspects of software-defined network and determines the areas that are prone to security attacks in the given software-defined network architecture. If the fundamental network topology information is poisoned, all the dependent network services will become immediately affected, causing catastrophic problems like host location hijacking attack, link fabrication attack, denial of service attack, man in the middle attack. These attacks affect the following features of SDN: availability, performance, integrity, and security. The flexibility in the programmability of control plane has both acted as a bane as well as a boon to SDN. Like the ARP poisoning in the legacy networks, there are several other vulnerabilities in the SDN architecture as well.

scholarly journals Behavioral interactions between a coexisting rodent Micaelamys namaquensis and macroscelid Elephantulus myurus

2010 ◽  
Vol 56 (4) ◽  
pp. 395-400 ◽  
Author(s):  
Jennifer Lancaster ◽  
Neville Pillay
Keyword(s):  
Species Coexistence ◽  
Interspecific Interactions ◽  
Behavioral Interactions ◽  
Direct Competition ◽  
Rocky Outcrop ◽  
Small Mammal Communities ◽  
Low Levels ◽  
Specialist Species ◽  
Mammal Communities

Abstract A number of mechanisms are known to influence coexistence in small mammal communities. However, the role of behavioral interactions in promoting species coexistence is under-represented in the literature. We studied the behavioral interactions of two coexisting small mammals, the Namaqua rock mouse Micaelamys namaquensis (Rodentia) and the Rock sengi Elephantulus myurus (Macroscelidae), which have high dietary and microhabitat overlap. Using wild-caught individuals, intra- and interspecific dyadic encounters were staged in tanks on a neutral rocky outcrop. Interspecific dyads displayed significantly more active avoidance behavior. There was no support for the prediction that the larger, more specialist species, E. myurus, is behaviorally dominant over M. namaquensis. Intraspecific encounters of E. myurus showed significantly more passive avoidance and amicable behavior, whereas the behavior of M. namaquensis did not differ between intra- and inter-specific encounters, both of which were characterized by low levels of aggression and amicability. Thus, due to the lack of aggression, direct competition appears weak and instead mutual avoidance may reduce or minimize interspecific interactions, potentially promoting coexistence.

scholarly journals My niche: individual spatial niche specialization affects within- and between-species interactions

2020 ◽  
Vol 287 (1918) ◽  
pp. 20192211 ◽  
Author(s):  
Annika Schirmer ◽  
Julia Hoffmann ◽  
Jana A. Eccard ◽  
Melanie Dammhahn
Keyword(s):  
Species Interactions ◽  
Community Dynamics ◽  
Species Coexistence ◽  
Myodes Glareolus ◽  
Ecological Niches ◽  
Species Variation ◽  
Interaction Patterns ◽  
Spatial Interactions ◽  
Interindividual Differences ◽  
Niche Specialization

Intraspecific trait variation is an important determinant of fundamental ecological interactions. Many of these interactions are mediated by behaviour. Therefore, interindividual differences in behaviour should contribute to individual niche specialization. Comparable with variation in morphological traits, behavioural differentiation between individuals should limit similarity among competitors and thus act as a mechanism maintaining within-species variation in ecological niches and facilitating species coexistence. Here, we aimed to test whether interindividual differences in boldness covary with spatial interactions within and between two ecologically similar, co-occurring rodent species ( Myodes glareolus , Apodemus agrarius ). In five subpopulations in northeast Germany, we quantified individual differences in boldness via repeated standardized tests and spatial interaction patterns via capture–mark–recapture ( n = 126) and automated VHF telemetry ( n = 36). We found that boldness varied with space use in both species. Individuals of the same population occupied different spatial niches, which resulted in non-random patterns of within- and between-species spatial interactions. Behavioural types mainly differed in the relative importance of intra- versus interspecific competition. Within-species variation along this competition gradient could contribute to maintaining individual niche specialization. Moreover, behavioural differentiation between individuals limits similarity among competitors, which might facilitate the coexistence of functionally equivalent species and, thus, affect community dynamics and local biodiversity.

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