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Guo, Xue, Huaqun Yin, Jing Cong, Zhimin Dai, Yili Liang, and Xueduan Liu. "RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage." Applied and Environmental Microbiology 79, no. 6 (January 18, 2013): 2019–26. http://dx.doi.org/10.1128/aem.03400-12.
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ABSTRACTThe enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-sixcbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities ofcbbLand the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.
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Humphreys, John M., Angela M. Pelzel-McCluskey, Lee W. Cohnstaedt, Bethany L. McGregor, Kathryn A. Hanley, Amy R. Hudson, Katherine I. Young, Dannele Peck, Luis L. Rodriguez, and Debra P. C. Peters. "Integrating Spatiotemporal Epidemiology, Eco-Phylogenetics, and Distributional Ecology to Assess West Nile Disease Risk in Horses." Viruses 13, no. 9 (September 12, 2021): 1811. http://dx.doi.org/10.3390/v13091811.
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Mosquito-borne West Nile virus (WNV) is the causative agent of West Nile disease in humans, horses, and some bird species. Since the initial introduction of WNV to the United States (US), approximately 30,000 horses have been impacted by West Nile neurologic disease and hundreds of additional horses are infected each year. Research describing the drivers of West Nile disease in horses is greatly needed to better anticipate the spatial and temporal extent of disease risk, improve disease surveillance, and alleviate future economic impacts to the equine industry and private horse owners. To help meet this need, we integrated techniques from spatiotemporal epidemiology, eco-phylogenetics, and distributional ecology to assess West Nile disease risk in horses throughout the contiguous US. Our integrated approach considered horse abundance and virus exposure, vector and host distributions, and a variety of extrinsic climatic, socio-economic, and environmental risk factors. Birds are WNV reservoir hosts, and therefore we quantified avian host community dynamics across the continental US to show intra-annual variability in host phylogenetic structure and demonstrate host phylodiversity as a mechanism for virus amplification in time and virus dilution in space. We identified drought as a potential amplifier of virus transmission and demonstrated the importance of accounting for spatial non-stationarity when quantifying interaction between disease risk and meteorological influences such as temperature and precipitation. Our results delineated the timing and location of several areas at high risk of West Nile disease and can be used to prioritize vaccination programs and optimize virus surveillance and monitoring.
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Brennan, Ian G., Alan R. Lemmon, Emily Moriarty Lemmon, Daniel M. Portik, Valter Weijola, Luke Welton, Stephen C. Donnellan, and J. Scott Keogh. "Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity." Systematic Biology 70, no. 1 (June 10, 2020): 120–32. http://dx.doi.org/10.1093/sysbio/syaa046.
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Abstract Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.]
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Vincent, Helvin, Harisree P. Nair, and Dr Sarita G. Bhat. "Community Genomics Involving Culture Independent Approach for Assessing the Phylogenetic Diversity of Mangrove Sediment." Indian Journal of Applied Research 3, no. 10 (October 1, 2011): 1–4. http://dx.doi.org/10.15373/2249555x/oct2013/10.
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Tofts, Richard, and Jonathan Silvertown. "A phylogenetic approach to community assembly from a local species pool." Proceedings of the Royal Society of London. Series B: Biological Sciences 267, no. 1441 (February 22, 2000): 363–69. http://dx.doi.org/10.1098/rspb.2000.1010.
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Hausberger, Barbara, and Judith Korb. "A phylogenetic community approach for studying termite communities in a West African savannah." Biology Letters 11, no. 10 (October 2015): 20150625. http://dx.doi.org/10.1098/rsbl.2015.0625.
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Termites play fundamental roles in tropical ecosystems, and mound-building species in particular are crucial in enhancing species diversity, from plants to mammals. However, it is still unclear which factors govern the occurrence and assembly of termite communities. A phylogenetic community approach and null models of species assembly were used to examine structuring processes associated with termite community assembly in a pristine savannah. Overall, we did not find evidence for a strong influence of interspecific competition or environmental filtering in structuring these communities. However, the presence of a single species, the mound-building termite Macrotermes bellicosus , left a strong signal on structuring and led to clustered communities of more closely related species. Hence, this species changes the assembly rules for a whole community. Our results show the fundamental importance of a single insect species for community processes, suggesting that more attention to insect species is warranted when developing conservation strategies.
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Smeti, Evangelia, Konstantinos Ar Kormas, and Sofie Spatharis. "A non-phylogenetic alpha diversity approach on prokaryotic community structure in aquatic systems." Ecological Indicators 29 (June 2013): 361–66. http://dx.doi.org/10.1016/j.ecolind.2013.01.027.
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Quattrini, Andrea M., Peter J. Etnoyer, Cheryl Doughty, Lisa English, Rosalia Falco, Natasha Remon, Matthew Rittinghouse, and Erik E. Cordes. "A phylogenetic approach to octocoral community structure in the deep Gulf of Mexico." Deep Sea Research Part II: Topical Studies in Oceanography 99 (January 2014): 92–102. http://dx.doi.org/10.1016/j.dsr2.2013.05.027.
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von Wintzingerode, Friedrich, Burkhard Selent, Werner Hegemann, and Ulf B. Göbel. "Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium." Applied and Environmental Microbiology 65, no. 1 (January 1, 1999): 283–86. http://dx.doi.org/10.1128/aem.65.1.283-286.1999.
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ABSTRACT A culture-independent phylogenetic survey for an anaerobic trichlorobenzene-transforming microbial community was carried out. Small-subunit rRNA genes were PCR amplified from community DNA by using primers specific for Bacteria or Euryarchaeotaand were subsequently cloned. Application of a new hybridization-based screening approach revealed 51 bacterial clone families, one of which was closely related to dechlorinating Dehalobacter species. Several clone sequences clustered to rDNA sequences obtained from a molecular study of an anaerobic aquifer contaminated with hydrocarbons and chlorinated solvents (Dojka et al., Appl. Env. Microbiol. 64:3869–3877, 1998).
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Delhaye, Guillaume, Olivier J. Hardy, Maxime Séleck, Edouard Ilunga wa Ilunga, Grégory Mahy, and Pierre Meerts. "Plant community assembly along a natural metal gradient in central Africa: Functional and phylogenetic approach." Journal of Vegetation Science 31, no. 1 (November 27, 2019): 151–61. http://dx.doi.org/10.1111/jvs.12829.
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Santos, Alisson Borges Miranda, Vinicius Andrade Maia, Cléber Rodrigo de Souza, Nathalle Cristine Alencar Fagundes, Fernanda Moreira Gianasi, Aurélio de Jesus Rodrigues Pais, Natália de Aguiar-Campos, et al. "Disentangling spatial, environmental and historical effects on tropical forest tree species turnover." Journal of Plant Ecology 14, no. 4 (March 26, 2021): 717–29. http://dx.doi.org/10.1093/jpe/rtab027.
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Abstract Aims We aimed at disentangling the effects of spatial distance, current and past environmental dissimilarity, and their combinations on tree community taxonomic and phylogenetic turnover by addressing the following questions: (i) Is tree community taxonomic and phylogenetic turnover related to the indirect effects of spatial distance via environmental dissimilarity? (ii) Does tree community taxonomic and phylogenetic turnover respond to paleoclimate (Last Glacial Maximum and Mid-Holocene)? Methods The study was carried out in 14 Atlantic rainforest sites in Brazil (20.4 ha sampled) containing 615 tree species from 83 plant families. We obtained plot-level geographic coordinates and soil variables and site-level bioclimatic variables in the current, Mid-Holocene and Last Glacial Maximum. We used structural equation models with a distance-based approach to (i) test the direct effects of spatial distance and environmental dissimilarity and (ii) test the indirect effects of spatial distance via environmental dissimilarity on taxonomic (Bray–Curtis distance) and phylogenetic turnover (Comdist and Comdistnt distances). Important Findings Our results suggest a weak indirect effect of spatial distance via environmental dissimilarity on taxonomic and phylogenetic turnover. Tree community turnover was driven by the direct effects of neutral, niche-based and historical processes. Thus, we inferred that the paleoclimate (historical processes) promoted the selection of the clades that gave rise to the current flora, while spatial distances (neutral processes) limited the dispersal range of species from the regional pool and environmental conditions (niche-based processes) locally selected the taxa that are able to persist.
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VAN DER MESCHT, LUTHER, IRINA S. KHOKHLOVA, ELIZABETH M. WARBURTON, and BORIS R. KRASNOV. "Revisiting the role of dissimilarity of host communities in driving dissimilarity of ectoparasite assemblages: non-linear vs linear approach." Parasitology 144, no. 10 (May 11, 2017): 1365–74. http://dx.doi.org/10.1017/s003118201700066x.
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SUMMARYWe revisited the role of dissimilarity of host assemblages in shaping dissimilarity of flea assemblages using a non-linear approach. Generalized dissimilarity models (GDMs) were applied using data from regional surveys of fleas parasitic on small mammals in four biogeographical realms. We compared (1) model fit, (2) the relative effects of host compositional and phylogenetic turnover and geographic distance on flea compositional and phylogenetic turnover, and (3) the rate of flea turnover along gradients of host turnover and geographic distance with those from earlier application of a linear approach. GDMs outperformed linear models in explaining variation in flea species turnover and host dissimilarity was the best predictor of flea dissimilarity, irrespective of scale. The shape of the relationships between flea compositional turnovers along host compositional turnover was similar in all realms, whereas turnover along geographic distance differed among realms. In contrast, the rate of flea phylogenetic turnover along gradients of host phylogenetic turnover differed among realms, whereas flea phylogenetic turnover did not depend on geographic distance in any realm. We demonstrated that a non-linear approach (a) explained spatial variation in parasite community composition better than and (b) revealed patterns that were obscured by earlier linear analyses.
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Presti, Alessandra Lo, Federica Del Chierico, Annamaria Altomare, Francesca Zorzi, Eleonora Cella, Lorenza Putignani, Michele Pier Luca Guarino, et al. "Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS." Future Microbiology 14, no. 17 (November 2019): 1497–509. http://dx.doi.org/10.2217/fmb-2019-0175.
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Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials & methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Results: Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. Conclusion: The genetic variation combined to the relative abundance, contribute to the protective role of A. muciniphila. Phylogenesis represent an additional approach to investigate genetic variability.
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Veldkornet, D. A., J. B. Adams, J. S. Boatwright, and A. Rajkaran. "Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline." Genome 62, no. 9 (September 2019): 585–95. http://dx.doi.org/10.1139/gen-2018-0067.
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Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.
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Podani, János, Sandrine Pavoine, and Carlo Ricotta. "A Generalized Framework for Analyzing Taxonomic, Phylogenetic, and Functional Community Structure Based on Presence–Absence Data." Mathematics 6, no. 11 (November 12, 2018): 250. http://dx.doi.org/10.3390/math6110250.
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Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits—a more or less subjective element of the framework—remains to be investigated.
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Emerson, Brent C., Francesco Cicconardi, Pietro P. Fanciulli, and Peter J. A. Shaw. "Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1576 (August 27, 2011): 2391–402. http://dx.doi.org/10.1098/rstb.2011.0057.
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There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.
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WIJAYANTI, MARINI, ARIS TRI WAHYUDI, MUNTI YUHANA, MARTIN ENGELHAUPT, and ANJA MERYANDINI. "Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia." Biodiversitas Journal of Biological Diversity 20, no. 3 (March 3, 2019): 811–18. http://dx.doi.org/10.13057/biodiv/d200326.
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Abstract. Wijayanti M, Wahyudi AT, Yuhana M, Engelhaupt M, Meryandini A. 2019. Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia. Biodiversitas 20: 811-818. Land use change from forest to oil palm plantation at Sumatra could decrease biodiversity, including bacterial diversity. The case of Bukit Dua Belas transformation from forest to oil palm plantation was gotten for measuring shift community of soil bacterial in both areas. The diversity of bacterial communities from rainforest and oil palm plantation topsoil in Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used to reveal the community shift of bacterial phyla and genera in both areas. Ecological approach was carried out by measuring soil pH, TC (total carbon), TN (total nitrogen), AP (available phosphorous), bacterial diversity with Shannon and Simpson indices, and bacterial richness with Chao1-ACE index and OTUs. Bacterial diversity and richness on lowland forest topsoil and oil palm plantation soil were not different, as soil pH, TC, and TN as substrate factors were not different significantly. The majority of sequences related to Acidobacteria (56.33%), Proteobacteria (27.43%), Actinobacteria (7.11%), and Cyanobacteria (5.55%) were from forest; whereas those related to Acidobacteria (50.11%), Proteobacteria (31.63%), Actinobacteria (7.58%), Chloroflexi (2.60%), and Gemmatimonadetes (2.71%) invented from oil palm plantation. Acidobacteria was the most dominant phyla in both habitats, because soil pH in both areas was acidic (3.77 - 4.80 pHH2O). The genera of alpha-proteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed in both forest and oil palm plantation topsoil. The most genera in phylogenetic tree are Burkholderia from Beta-proteobacteria. The bacterial community shift occurred in forest transformation, even though the oil palm plantation showed more bacterial phyla and genera than the lowland rainforest.
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Lin, Bin, Carlos M. Monreal, James T. Tambong, Carlos B. Miguez, and Lorna Carrasco-Medina. "Phylogenetic analysis of methanotrophic communities in cover soils of a landfill in Ontario." Canadian Journal of Microbiology 55, no. 9 (September 2009): 1103–12. http://dx.doi.org/10.1139/w09-069.
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We examined the methanotrophs in the Trail Road Landfill soils, Ottawa, Ontario, through cultivation-independent molecular assay and the culturing approach. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified methanotroph-specific 16S rDNA gene fragments revealed a more diverse type I (RuMP pathway) methanotrophic community than type II (serine pathway) in 17 soil samples taken along a 50 m transect. The type II methanotrophic community was less diverse, with the dominance of Methylocystis in almost all samples, and clustering with high similarity (85%–88%). Also, the results showed that the C/N ratio of soil organic matter could significantly affect the methanotrophic community structures. The DGGE results were supported by sequence analysis of cloned pmoA. Members of the genera Methylobacter (type I), Methylocaldum (type X), and Methylocystis (type II) appeared to be the dominant methanotrophs. From methanotrophic enrichments, we isolated type I Methylobacter sp., and 3 type II Methylocystis spp.,which appeared to be one of the dominant bacteria species in the soil sample from which isolates were obtained.
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Casalla Daza, Robin, and Judith Korb. "Phylogenetic Community Structure and Niche Differentiation in Termites of the Tropical Dry Forests of Colombia." Insects 10, no. 4 (April 10, 2019): 103. http://dx.doi.org/10.3390/insects10040103.
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The mechanisms that structure species communities are still debated. We addressed this question for termite assemblages from tropical dry forests in Colombia. These forests are endangered and poorly understood ecosystems and termites are important ecosystem engineers in the tropics. Using biodiversity and environmental data, combined with phylogenetic community analyses, trait mapping, and stable isotopes studies, we investigated the termite community composition of three protected dry forests in Colombia. Our data suggest that the structuring mechanisms differed between sites. Phylogenetic overdispersion of termite assemblages correlated with decreasing rainfall and elevation and increasing temperature. Food niche traits—classified as feeding groups and quantified by δ15N‰ and δ13C‰ isotope signatures—were phylogenetically conserved. Hence, the overdispersion pattern implies increasing interspecific competition with decreasing drier and warmer conditions, which is also supported by fewer species occurring at the driest site. Our results are in line with a hypothesis that decreased biomass production limits resource availability for termites, which leads to competition. Along with this comes a diet shift: termites from drier plots had higher δ13C signatures, reflecting higher δ13C values in the litter and more C4 plants. Our study shows how a phylogenetic community approach combined with trait analyses can contribute to gaining the first insights into mechanisms structuring whole termite assemblages.
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Lam, Tony J., Moses Stamboulian, Wontack Han, and Yuzhen Ye. "Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species." PLOS Computational Biology 16, no. 10 (October 30, 2020): e1007951. http://dx.doi.org/10.1371/journal.pcbi.1007951.
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Microbial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of cooperative and competitive metabolic interactions between bacterial species. By nature, phylogenetically similar microbial species are more likely to share common functional profiles or biological pathways due to their genomic similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation between species based on functional/pathway profiles may bias downstream applications. To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut associated bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.
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Wijayanti, Marini, Aris Tri Wahyudi, Munti Yuhana, Martin Engelhaupt, and Anja Meryandini. "Bacterial Communities in Aquatic Sediment from Bukit Duabelas Raintforest and Oil Palm Plantation at Sumatra Indonesia." HAYATI Journal of Biosciences 25, no. 2 (October 9, 2018): 85. http://dx.doi.org/10.4308/hjb.25.2.85.
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The diversity of bacterial communities in aquatic sediment of rainforest and oil palm plantation at Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used for revealing the community shift of bacterial phyla and genera in both areas. Ecological approach used soil pH, total Carbon (TC), total Nitrogen (TN), available Phosphorus (AP) measurement and bacterial diversity with Shanon and Simpson indices, and bacterial richness with Chao1-ACE indices and OTUs. Bacterial diversity and richness in aquatic sediment of forest area was higher than that ones in oil palm plantation area, although their pH, TC, and TN in both areas were not different significantly. The majority of sequences related to Proteobacteria (34.85%), Acidobacteria (32.67%), Nitrospirae (6.86%), Chloroflexi (4.31%), and Actinobacteria (4.02%) were from forest; whereas those related to Acidobacteria (46.10%), Proteobacteria (25.86%), Nitrospirae (9.20%), Chloroflexi (4.99%), and Actinobacteria (2.34%) invented from oil palm plantation. The genera of Alphaproteobacteria and Betaproteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed both aquatic sediment of forest and oil palm plantation. The most genera in the phylogenetic tree from aquatic sediment of both areas was Burkholderia. The bacterial community shift in aquatic sediment of forest transformation indicated higher bacterial diversity index, richness index, some of phyla and genera in aquatic sediment from forest than from oil palm plantation.
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Mukti, Roushney Fatima, and Sanjida Sakhawat Sinthee. "Metagenomic Approach: Transforming In-Silico Research for Improved Biogas Production." International Journal of Applied Sciences and Biotechnology 7, no. 1 (March 27, 2019): 6–11. http://dx.doi.org/10.3126/ijasbt.v7i1.23315.
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The complexity of the microbial communities and metabolic pathways involved in the microbiological process of biogas production is poorly understood and numerous microorganisms in the fermentation sample of the biogas plant are still unclassified or unknown. The structure and function of microbial communities and the effects of the addition of trace elements are needed to be known, to control and channel the energy sources microbes produce and to capture and store the useful by-products or for targeted screening of novel enzymes. In this review, we discussed an emerging idea that Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production. The composition and gene content of a biogas-producing consortium can be determined through metagenomic approach which allows the design of the optimal microbial community structure for any biogas plant for the significant progress in the efficacy and economic improvement of biogas production and biofertilizer of either balanced nutrition or rich in specific element for plant growth produced from the sludge of biogas plant. Biogas-producing microbial community from different production-scale biogas plants supplied with different raw materials as substrates can be analyzed by polyphasic approach to find out the best raw material composition for biogas production. The phylogenetic structure of the microbial community residing in a fermentation sample from a biogas plant can be analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing.
Int. J. Appl. Sci. Biotechnol. Vol 7(1): 6-11
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MUSTAFA, ROZINA GHULAM, SAIQA ANDLEEB, JORGE DOMÍNGUEZ, WAJID ARSHAD ABBASI, SHAUKAT ALI, and DANIEL FERNÁNDEZ MARCHÁN. "New Earthworm Record from Division Muzaffarabad, Azad Kashmir, Pakistan Supported by Molecular Markers." Zootaxa 5255, no. 1 (March 15, 2023): 93–100. http://dx.doi.org/10.11646/zootaxa.5255.1.13.
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Earthworm diversity and ecology in Pakistan is poorly known, especially in the region of Azad Jammu & Kashmir. An earthworm community survey assisted by genetic barcoding detected an unidentified species which could constitute a new record for Pakistan. Morphological study revealed its identity as Perelia kaznakovi. Additionally, Bayesian phylogenetic inference based on five mitochondrial and nuclear molecular markers was performed. Results provided a phylogenetic placement of the genus Perelia within Lumbricidae for the first time, indicating a close relationship with Eophila. This approach should be implemented to Perelia arnoldiana and further representatives of the genus in order to understand their biogeography, diversity and evolutionary history.
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Youssef, Noha, Brandi L. Steidley, and Mostafa S. Elshahed. "Novel High-Rank Phylogenetic Lineages within a Sulfur Spring (Zodletone Spring, Oklahoma), Revealed Using a Combined Pyrosequencing-Sanger Approach." Applied and Environmental Microbiology 78, no. 8 (February 3, 2012): 2677–88. http://dx.doi.org/10.1128/aem.00002-12.
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ABSTRACTThe utilization of high-throughput sequencing technologies in 16S rRNA gene-based diversity surveys has indicated that within most ecosystems, a significant fraction of the community could not be assigned to known microbial phyla. Accurate determination of the phylogenetic affiliation of such sequences is difficult due to the short-read-length output of currently available high-throughput technologies. This fraction could harbor multiple novel phylogenetic lineages that have so far escaped detection. Here we describe our efforts in accurate assessment of the novelty and phylogenetic affiliation of selected unclassified lineages within a pyrosequencing data set generated from source sediments of Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma. Lineage-specific forward primers were designed for 78 putatively novel lineages identified within the pyrosequencing data set, and representative nearly full-length small-subunit (SSU) rRNA gene sequences were obtained by pairing those primers with reverse universal bacterial primers. Of the 78 lineages tested, amplifiable products were obtained for 52, 32 of which had at least one nearly full-length sequence that was representative of the lineage targeted. Analysis of phylogenetic affiliation of the obtained Sanger sequences identified 5 novel candidate phyla and 10 novel candidate classes (withinFibrobacteres,Planctomycetes, and candidate phyla BRC1, GN12, TM6, TM7, LD1, WS2, and GN06) in the data set, in addition to multiple novel orders and families. The discovery of multiple novel phyla within a pilot study of a single ecosystem clearly shows the potential of the approach in identifying novel diversities within the rare biosphere.
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Gómez, Juan Pablo, Gustavo A. Bravo, Robb T. Brumfield, José G. Tello, and Carlos Daniel Cadena. "A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds." Journal of Animal Ecology 79, no. 6 (July 20, 2010): 1181–92. http://dx.doi.org/10.1111/j.1365-2656.2010.01725.x.
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GUTIÉRREZ, P. A. "Monogenean community structure on the gills of Pimelodus albicans from Río de la Plata (Argentina): a comparative approach." Parasitology 122, no. 4 (April 2001): 465–70. http://dx.doi.org/10.1017/s003118200100748x.
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The community structure of monogeneans on the gills of a catfish Pimelodus albicans, in the Río de la Plata, was studied and compared with previous findings on P. maculatus. Six Monogenea species belonging to 3 genera were found: Demidospermus majusculus Kritsky & Gutiérrez, 1998; Demidospermus armostus Kritsky & Gutiérrez, 1998; Demidospermus idolus Kritsky & Gutiérrez, 1998; Demidospermus bidiverticulatum (Suriano & Incorvaia, 1995) Kritsky & Gutiérrez, 1998; Scleroductus yuncensi Jara & Cone, 1989; and Unibarra paranoplatensis Suriano & Incorvaia, 1995. The relationships between selected host and helminth variables; the interactions between the worms and the patterns obtained from the species abundance were analysed employing appropriate statistical methodology. The results obtained revealed the following common patterns within the monogenean communities of P. maculatus and P. albicans: (a) most monogenean species belonged to the genus Demidospermus; (b) S. yuncensi was a secondary species in both communities; (c) 1 of the 3 species common to both hosts was a core species (D. bidiverticulatum); (d) the selected variables of both hosts (weight and length) were not related to the number of monogeneans or species richness; (e) the dominant species in both communities showed the highest proportion of monogeneans in more than 40 % of the infracommunities; (f ) in both communities the dominant species accounted for 40–80 % of the total number of monogeneans at component community level; (g) the number of worms correlates positively with the species richness; (h) few cases of interaction among species were found; (i) a high degree of order exists among the infracommunities compared. Finally, the proportion of common species and the phylogenetic and ecological resemblances between the hosts, P. maculatus and P. albicans support a hypothesis of co-speciation among monogeneans and pimelodids in Río de la Plata. It seems improbable that these parasite communities are recent species assemblages formed by chance. The phylogenetic resemblance of the host–monogeneans system in Río de la Plata suggests that there is a single community pattern that can be observed in congeneric and sympatric hosts.
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Hsiang, Allison Y., Leanne E. Elder, and Pincelli M. Hull. "Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1691 (April 5, 2016): 20150227. http://dx.doi.org/10.1098/rstb.2015.0227.
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With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct ‘look’ to communities—making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera—an abundant group in the marine fossil record—and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic.
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Reiter, Birgit, and Angela Sessitsch. "Bacterial endophytes of the wildflowerCrocus albiflorusanalyzed by characterization of isolates and by a cultivation-independent approach." Canadian Journal of Microbiology 52, no. 2 (February 1, 2006): 140–49. http://dx.doi.org/10.1139/w05-109.
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The presence and taxonomy of endophytic bacteria of the entire aerial parts of crocus (Crocus albiflorus), a wildflower native in the Alps, were investigated. A combination of plating of plant macerates, isolation and sequence identification of isolates, and direct 16S rDNA PCR amplification followed by whole-community fingerprinting (T-RFLP) and by construction of a bacterial clone library was used. The results clearly indicated that a wide range of bacteria from diverse phylogenetic affiliation, mainly γ-Proteobacteria and Firmicutes, live in association with plants of C. albiflorus. The community composition of the culturable component of the microflora was remarkably different from that of the clone library. Only three bacterial divisions were found in the culture collection, which represented 17 phylotypes, whereas six divisions were identified in the clonal analysis comprising 38 phylotypes. The predominant group in the culture collection was the low G + C Gram-positive group, whereas in the clone library, the γ-Proteobacteria predominated. Interestingly, the most prominent bacterium within the uncultured bacterial community was a pseudo monad closely related to a cold-tolerant Pseudomonas marginalis strain. The results suggest that Crocus supports a diverse bacterial microflora resembling the microbial communities that have been described for other plants and containing species that have not been described in association with plants.Key words: crocus, endophytes, 16S rRNA, 16S rDNA clone library, T-RFLP analysis, community analysis.
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Yao, Liangjin, Yue Xu, Chuping Wu, Fuying Deng, Lan Yao, Xunru Ai, and Runguo Zang. "Community Assembly of Forest Vegetation along Compound Habitat Gradients across Different Climatic Regions in China." Forests 13, no. 10 (September 29, 2022): 1593. http://dx.doi.org/10.3390/f13101593.
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Community assembly research has mostly focused on areas with single vegetation types; however, the abiotic and biotic factors affecting community assembly act across regions. Integrating biotic and abiotic factors into “compound” habitats has gained attention as an emerging strategy to analyze spatial and temporal patterns of biodiversity. We used a compound habitat approach to explore the relative roles of habitat filtering, biotic competition, and stochastic processes in the forest community assembly of four climatic zones (tropical, subtropical, temperate, and cold temperate forests). Specifically, we combined biotic and abiotic factors in four compound ecological gradients by principal component analysis (PCA), which we used to assess the geographic and phylogenetic distribution of multiple woody plant functional traits. We found that forest functional and phylogenetic diversity shifted from clustered to overdispersed along the first compound habitat gradient (PC1) across climate zones. This finding indicates that competitive exclusion strongly affected the community assembly in tropical and subtropical forests, while habitat filtering played a key role in cold temperate forests; these mechanisms may both exist and interact in temperate forests. We also found that both habitat filtering and biotic competition affected forest community assembly across climatic regions in China. Our results elucidate the underlying mechanisms driving geographical differentiation of forest vegetation across climatic zones, and bolster empirical evidence for the conservation of forest biodiversity in China. Further research is also needed to explore whether the patterns found in this paper are prevalent in different locations in different climatic zones in China.
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Gilbert, Gregory S., and Ingrid M. Parker. "Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves." Diversity 14, no. 7 (June 28, 2022): 521. http://dx.doi.org/10.3390/d14070521.
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The phylogenetic distance between species often predicts differences in ecologically important traits. The phylogenetic diversity and structure of biological communities can inform our understanding of the processes that shape those communities, and there is a well-developed framework for comparing phylogenetic structures of communities. However, particularly in studies of phylogenetic distances from one focal species to other members of its assemblage (a one-to-many framework), the standard metrics of community-wide studies encounter significant limitations due to the left-skewed distribution of pairwise phylogenetic distances in most biological communities. For studies that require estimating the degree of phylogenetic isolation of a focal taxon, the mean phylogenetic distance (MPD) usually provides little power to distinguish among taxa because it is heavily weighted by the many ways to be distantly related, whereas the nearest taxon distance (NTD) is highly idiosyncratic and ignores cases where multiple close relatives may contribute equally strongly to influence the focal species. Here we highlight the value of examining the cumulative distribution of phylogenetic distances in studies that take a focal-species approach. We describe and discuss the benefits of two new metrics. An integrated metric of phylogenetic distances (AUPhyDC) uses information from the whole cumulative distribution, whereas the tenth quantile (PD10) is an extremely simple metric that improves on NTD by capturing the influence of multiple close relatives on ecological interactions. Several recent examples found that PD10 did a better job of revealing ecological patterns than NTD or MPD. We provide R code to facilitate the use of these approaches and advocate for the inclusion of PD10 along with NTD and MPD in statistical packages for phylogenetic ecology.
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Sommer, Brigitte, Eugenia M. Sampayo, Maria Beger, Peter L. Harrison, Russ C. Babcock, and John M. Pandolfi. "Local and regional controls of phylogenetic structure at the high-latitude range limits of corals." Proceedings of the Royal Society B: Biological Sciences 284, no. 1861 (August 23, 2017): 20170915. http://dx.doi.org/10.1098/rspb.2017.0915.
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Understanding how range-edge populations will respond to climate change is an urgent research priority. Here, we used a phylogenetic community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of scleractinian corals at their high-latitude range limits in eastern Australia. We estimated phylogenetic signal in seven ecologically important functional traits and conducted tests of phylogenetic structure at local and regional scales using the net relatedness (NRI) and nearest taxon indices (NTI) for the presence/absence and abundance data. Regional tests showed light phylogenetic clustering, indicating that coral species found in this subtropical-to-temperate transition zone are more closely related to each other than are species on the nearby, more northerly Great Barrier Reef. Local tests revealed variable patterns of phylogenetic clustering and overdispersion and higher than expected phylogenetic turnover among sites. In combination, these results are broadly consistent with the hierarchical filtering model, whereby species pass through a regional climatic filter based on their tolerances for marginal conditions and subsequently segregate into local assemblages according to the relative strength of habitat filtering and species interactions. Conservatism of tested traits suggests that corals will likely track their niches with climate change. Nevertheless, high turnover of lineages among sites indicates that range shifts will probably vary among species and highlights the vulnerability and conservation significance of high-latitude reefs.
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Isobe, Kazuo, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, and Jennifer B. H. Martiny. "Phylogenetic conservation of soil bacterial responses to simulated global changes." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1798 (March 23, 2020): 20190242. http://dx.doi.org/10.1098/rstb.2019.0242.
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Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO 2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
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Borges, Dérick Gabriel F., Daniel S. Carvalho, Gilberto C. Bomfim, Pablo Ivan P. Ramos, Jerzy Brzozowski, Aristóteles Góes-Neto, Roberto Andrade, and Charbel El-Hani. "On the origin of mitochondria: a multilayer network approach." PeerJ 11 (January 6, 2023): e14571. http://dx.doi.org/10.7717/peerj.14571.
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Backgound The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method. Methods We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa. Results In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades. Conclusion By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.
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Alam, Sk Aftabul, and Pradipta Saha. "Functional, and phylogenetic analysis of maleylacetate reductase of Pseudomonas sp strain PNPG3: An in-silico approach." Journal of Experimental Biology and Agricultural Sciences 10, no. 6 (December 31, 2022): 1331–43. http://dx.doi.org/10.18006/2022.10(6).1331.1343.
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Shrinking freshwater ecosystems are under tremendous pollution threat due to anthropocentric activities. Para nitrophenol (PNP), a well-documented priority pollutant extensively used in dyes, petrochemical, pharmaceutical, explosives, pesticides, leather industries, and agrochemicals, is responsible for contaminating aquatic ecosystems globally. It is highly toxic and has carcinogenic and mutagenic effects on living organisms like humans and several animal models. Bioremediation approaches mainly involving bacteria are considered the best, most eco-friendly, cost-effective, green, and clean method for effective removal PNP from its contaminated sites. This manuscript highlights the structural and functional analysis of a lower pathway enzyme involved in PNP degradation, maleylacetate reductase (MR), from Pseudomonas sp strain PNPG3, which was recently isolated from a freshwater ecosystem. This enzyme plays a role in converting maleylacetate to 3-oxoadipate. Despite its crucial functional role, no model is available for this protein in the protein database (PDB). Therefore, attempts were made for the computational investigation of physicochemical, functional, and structural properties, including secondary, and tertiary structure prediction, model quality analysis, and phylogenetic assessment using several standard bioinformatics tools. This enzyme has a molecular weight of about ~37.6 kDa, is acidic and thermostable, belonging to a member of iron-containing alcohol dehydrogenase. Moreover, this study will benefit the scientific community in deciphering the prediction of the function of similar proteins of interest.
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Dedysh, Svetlana N., Timofei A. Pankratov, Svetlana E. Belova, Irina S. Kulichevskaya, and Werner Liesack. "Phylogenetic Analysis and In Situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog." Applied and Environmental Microbiology 72, no. 3 (March 2006): 2110–17. http://dx.doi.org/10.1128/aem.72.3.2110-2117.2006.
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ABSTRACT The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3 × 107 and 1.1 × 107 cells g−1 peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.
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SASAL, P., N. NIQUIL, and P. BARTOLI. "Community structure of digenean parasites of sparid and labrid fishes of the Mediterranean sea: a new approach." Parasitology 119, no. 6 (December 1999): 635–48. http://dx.doi.org/10.1017/s0031182099005077.
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The aim of this work was to study the structure of the parasite communities of Digeneans of 2 families of Teleost fishes (Sparidae and Labridae) of the Mediterranean sea. We tried to quantify the importance of both the microhabitat requirements of the parasite species and the effect of host biological factors on the parasite communities. We applied, for the first time in parasite community studies, the Canonical Correspondence Analysis (CCA) to analyse (i) the spatial distribution of parasite species within the digestive tract of the hosts; (ii) the host's biological factors (such as diet, host length, gregariousness and abundance) that may influence this spatial distribution of parasite species. Our results showed that potential microhabitats were vacant in the 2 host families studied revealing a lack of niche saturation because either there was little inter- and/or intraspecific competition or there were enough available space and resources within the host. Our results also indicated that the position of the parasite in the digestive tract is much more important than host biological factors for the structure of parasite community. Finally, we highlight the potential use of the CCA method for controlling for phylogenetic constraints in multi-species analyses.
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Liu, Jun, Zheng-Shuang Hua, Lin-Xing Chen, Jia-Liang Kuang, Sheng-Jin Li, Wen-Sheng Shu, and Li-Nan Huang. "Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings." Applied and Environmental Microbiology 80, no. 12 (April 11, 2014): 3677–86. http://dx.doi.org/10.1128/aem.00294-14.
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ABSTRACTRecent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within theAlphaproteobacteria,Deltaproteobacteria, andFirmicuteswere attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.
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Tripathi, Richa, Amit Reza, Adam Mertel, Guohuan Su, and Justin M. Calabrese. "A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins." PLOS ONE 18, no. 6 (June 23, 2023): e0287482. http://dx.doi.org/10.1371/journal.pone.0287482.
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The complex network framework has been successfully used to model interactions between entities in Complex Systems in the Biological Sciences such as Proteomics, Genomics, Neuroscience, and Ecology. Networks of organisms at different spatial scales and in different ecosystems have provided insights into community assembly patterns and emergent properties of ecological systems. In the present work, we investigate two questions pertaining to fish species assembly rules in US river basins, a) if morphologically similar fish species also tend to be phylogenetically closer, and b) to what extent are co-occurring species that are phylogenetically close also morphologically similar? For the first question, we construct a network of Hydrologic Unit Code 8 (HUC8) regions as nodes with interaction strengths (edges) governed by the number of common species. For each of the modules of this network, which are found to be geographically separated, there is differential yet significant evidence that phylogenetic distance predicts morphological distance. For the second question, we construct and analyze nearest neighbor directed networks of species based on their morphological distances and phylogenetic distances. Through module detection on these networks and comparing the module-level mean phylogenetic distance and mean morphological distance with the number of basins of common occurrence of species in modules, we find that both phylogeny and morphology of species have significant roles in governing species co-occurrence, i.e. phylogenetically and morphologically distant species tend to co-exist more. In addition, between the two quantities (morphological distance and phylogentic distance), we find that morphological distance is a stronger determinant of species co-occurrences.
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Merkel, Alexander Y., Nikolay A. Chernyh, Nikolai V. Pimenov, Elizaveta A. Bonch-Osmolovskaya, and Alexander I. Slobodkin. "Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane." Life 11, no. 9 (September 11, 2021): 953. http://dx.doi.org/10.3390/life11090953.
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Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.
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Monchamp, Marie-Eve, Jean-Claude Walser, Francesco Pomati, and Piet Spaak. "Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes." Applied and Environmental Microbiology 82, no. 21 (August 26, 2016): 6472–82. http://dx.doi.org/10.1128/aem.02174-16.
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ABSTRACTWe reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific toCyanobacteriarevealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termedMelainabacteria, which shares common ancestry withCyanobacteriaand has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjustedR2= 0.89;P< 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness ofChroococcalesandSynechococcalesmay be underestimated by microscopy. PCR detection of the microcystin synthetase genemcyAconfirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales.IMPORTANCECyanobacterial blooms can produce toxins that affect water quality, especially under eutrophic conditions, which are a consequence of human-induced climate warming and increased nutrient availability. Lakes worldwide have suffered from regular cyanobacterial blooms over the last century. The lack of long-term data limits our understanding of how these blooms form. We successfully reconstructed the past diversity of whole cyanobacterial communities over two hundred years by sequencing genes preserved in the sediments of two perialpine lakes in Switzerland. We identified changes in diversity over time and validated our results using existing data collected in the same two lakes over the past 40 years. This work shows the potential of our approach for addressing important ecological questions about the effects of a changing environment on lake ecology.
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Cisneros, Laura M., Matthew E. Fagan, and Michael R. Willig. "Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes." PeerJ 4 (October 13, 2016): e2551. http://dx.doi.org/10.7717/peerj.2551.
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BackgroundAssembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes.MethodsWe employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms.ResultsThe unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition.DiscussionVariation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.
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Jensen, Paul R., Philip G. Williams, Dong-Chan Oh, Lisa Zeigler, and William Fenical. "Species-Specific Secondary Metabolite Production in Marine Actinomycetes of the Genus Salinispora." Applied and Environmental Microbiology 73, no. 4 (December 8, 2006): 1146–52. http://dx.doi.org/10.1128/aem.01891-06.
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ABSTRACT Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.
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Liu, Jianyin, Mengjun Peng, and Youguo Li. "Phylogenetic diversity of nitrogen-fixing bacteria and thenifHgene from mangrove rhizosphere soil." Canadian Journal of Microbiology 58, no. 4 (April 2012): 531–39. http://dx.doi.org/10.1139/w2012-016.
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Nine types of nitrogen-fixing bacterial strains were isolated from 3 rhizosphere soil samples taken from mangrove plants in the Dongzhaigang National Mangrove Nature Reserve of China. Most isolates belonged to Gammaproteobacteria Pseudomonas , showing that these environments constituted favorable niches for such abundant nitrogen-fixing bacteria. New members of the diazotrophs were also found. Using a soil DNA extraction and PCR-cloning-sequencing approach, 135 clones were analyzed by restriction fragment length polymorphism (RFLP) analysis, and 27 unique nifH sequence phylotypes were identified, most of which were closely related to sequences from uncultured bacteria. The diversity of nitrogen-fixing bacteria was assessed by constructing nifH phylogenetic trees from sequences of all isolates and clones in this work, together with related nifH sequences from other mangrove ecosystems in GenBank. The nifH diversity varied among soil samples, with distinct biogeochemical properties within a mangrove ecosystem. When comparing different mangrove ecosystems, the nifH gene sequences from a specific site tended to cluster as individual groups. The results provided interesting data and novel information on our understanding of diazotroph community diversity in the mangrove ecosystems.
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Papale, Maria, Carmen Rizzo, Stefania Giannarelli, Gabriella Caruso, Stefano Amalfitano, Paul Eric Aspholm, Giovanna Maimone, et al. "Benthic Microbial Communities in a Seasonally Ice-Covered Sub-Arctic River (Pasvik River, Norway) Are Shaped by Site-Specific Environmental Conditions." Microorganisms 10, no. 5 (May 12, 2022): 1022. http://dx.doi.org/10.3390/microorganisms10051022.
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The Pasvik River experiences chemical, physical, and biological stressors due to the direct discharges of domestic sewage from settlements located within the catchment and runoff from smelter and mine wastes. Sediments, as a natural repository of organic matter and associated contaminants, are of global concern for the possible release of pollutants in the water column, with detrimental effects on aquatic organisms. The present study was aimed at characterizing the riverine benthic microbial community and evaluating its ecological role in relation to the contamination level. Sediments were sampled along the river during two contrasting environmental periods (i.e., beginning and ongoing phases of ice melting). Microbial enzymatic activities, cell abundance, and morphological traits were evaluated, along with the phylogenetic community composition. Amplified 16S rRNA genes from bacteria were sequenced using a next-generation approach. Sediments were also analyzed for a variety of chemical features, namely particulate material characteristics and concentration of polychlorobiphenyls, polycyclic aromatic hydrocarbons, and pesticides. Riverine and brackish sites did not affect the microbial community in terms of main phylogenetic diversity (at phylum level), morphometry, enzymatic activities, and abundance. Instead, bacterial diversity in the river sediments appeared to be influenced by the micro-niche conditions, with differences in the relative abundance of selected taxa. In particular, our results highlighted the occurrence of bacterial taxa directly involved in the C, Fe, and N cycles, as well as in the degradation of organic pollutants and toxic compounds.
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Flood, Janine A., Nicholas J. Ashbolt, and Peter C. Pollard. "Complementary independent molecular, radioisotopic and fluorogenic techniques to assess biofilm communities in two wastewater wetlands." Water Science and Technology 39, no. 7 (April 1, 1999): 65–70. http://dx.doi.org/10.2166/wst.1999.0329.
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Optimisation of nutrient removal processes requires a detailed understanding of the microbial physiologies actually occurring within the biomass of different treatment zones, and also knowledge of how these communities respond to environmental factors. This paper describes a suite of four independent and complementary, microbiological techniques, utilised to obtain detailed assessments of wastewater bacterial biomass. Examples of these techniques are shown as applied to biofilms from two surface-flow wetlands used for treating sewage effluent. Intact biofilms were prepared via freezing, followed by cryosectioning and direct microscopic observation. This approach was combined with prior, in situ incubation of biofilm with radiolabelled thymidine to assess in situ bacterial growth rates. Individual bacterial cells were assessed microscopically for in situ respiratory activity and phylogenetic identity, respectively through use of an inducibly-fluorescent redox stain (CTC), and fluorescent in situ hybridisation (FISH) of ribosomal RNA (rRNA). These complementary techniques enabled assessment of individual biofilm clusters according to their in situ status (growth, respiration, spatial location and phylogenetic affiliation). This approach detected significant spatial variations in biofilm; limited the bias inherent in data obtained using any one technique, and provided greater detail of subpopulations within the microbial community.
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Panyushkina, Anna, Maxim Muravyov, and Natalya Fomchenko. "A Case of Predominance of Alicyclobacillus tolerans in Microbial Community during Bioleaching of Pentlandite-Chalcopyrite Concentrate." Minerals 12, no. 4 (March 23, 2022): 396. http://dx.doi.org/10.3390/min12040396.
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Bacterial isolates assigned to the species Alicyclobacillus tolerans, which occupies an intermediate position between an organotrophic genus Alicyclobacillus and mixotrophic genus Sulfobacillus, were revealed as members of the acidophilic chemolithotrophic community during stirred-tank bioleaching of violarite–pentlandite–chalcopyrite concentrate at 40 °C. Surprisingly, this species succeeded more common iron-oxidizing community members after a series of bioleaching processes in bioreactors. The possibility of mixotrophic and organoheterotrophic growth of Al. tolerans, tolerance to low pH values (1.0–1.15), as well as preservation of cells via sporulation under unfavorable conditions, may explain its key role in the bioleaching of the copper–nickel bulk concentrate. Isolation of two other sulfur-oxidizing pure cultures dominating the microbial community, together with their phylogenetic characterization, allowed the assignment of these isolates to the species Acidithiobacillus caldus. This and other studies of acidophilic microbial communities are important for the development and intensification of the bioleaching processes, including a biobeneficiation approach previously proposed by us.
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Brodie, Eoin L., Todd Z. DeSantis, Dominique C. Joyner, Seung M. Baek, Joern T. Larsen, Gary L. Andersen, Terry C. Hazen, et al. "Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation." Applied and Environmental Microbiology 72, no. 9 (September 2006): 6288–98. http://dx.doi.org/10.1128/aem.00246-06.
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ABSTRACT Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as Geothrix fermentans (confirmed by quantitative PCR) and those within the Geobacteraceae were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner.
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Kleinsteuber, Sabine, Volker Riis, Ingo Fetzer, Hauke Harms, and Susann M�ller. "Population Dynamics within a Microbial Consortium during Growth on Diesel Fuel in Saline Environments." Applied and Environmental Microbiology 72, no. 5 (May 2006): 3531–42. http://dx.doi.org/10.1128/aem.72.5.3531-3542.2006.
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ABSTRACT The diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near Comodoro Rivadavia in Patagonia (Argentina) were investigated. Community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% NaCl were monitored by single-strand conformation polymorphism community fingerprinting of the PCR-amplified V4-V5 region of the 16S rRNA genes. Information obtained by this qualitative approach was extended by flow cytometric analysis to follow quantitatively the dynamics of community structures at different salinities. Dominant and newly developing clusters of individuals visualized via their DNA patterns versus cell sizes were used to identify the subcommunities primarily involved in the degradation process. To determine the most active species, subcommunities were separated physically by high-resolution cell sorting and subsequent phylogenetic identification by 16S rRNA gene sequencing. Reduced salinity favored the dominance of Sphingomonas spp., whereas at elevated salinities, Ralstonia spp. and a number of halophilic genera, including Halomonas, Dietzia, and Alcanivorax, were identified. The combination of cytometric sorting with molecular characterization allowed us to monitor community adaptation and to identify active and proliferating subcommunities.
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SOARES, FABIANA, IGOR TIAGO, JOÃO TROVÃO, CATARINA COELHO, NUNO MESQUITA, FRANCISCO GIL, LÍDIA CATARINO, SUSANA M. CARDOSO, and ANTÓNIO PORTUGAL. "Description of Myxacorys almedinensis sp. nov. (Synechococcales, Cyanobacteria) isolated from the limestone walls of the Old Cathedral of Coimbra, Portugal (UNESCO World Heritage Site)." Phytotaxa 419, no. 1 (September 30, 2019): 77–90. http://dx.doi.org/10.11646/phytotaxa.419.1.5.
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Cyanobacteria are photoautotrophic microorganisms able to colonize historic stone monuments, causing severe aesthetic, physical and chemical alterations to the substrate. In a study that aimed to fingerprint the phototrophic community of the biodeteriorated walls of the Old Cathedral of Coimbra (UNESCO World Heritage Site), an unknown Myxacorys-like cyanobacterium was isolated. In this paper, we employed a polyphasic approach based on morphological, ecological and phylogenetic analyses of the partial 16S and the whole 16S-23S ITS rRNA regions. The resulting analyses allowed us to propose the description of a new species, Myxacorys almedinensis sp. nov. within the genus Myxacorys.
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Sass, Chodon, William J. D. Iles, Craig F. Barrett, Selena Y. Smith, and Chelsea D. Specht. "Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage." PeerJ 4 (January 21, 2016): e1584. http://dx.doi.org/10.7717/peerj.1584.
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The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order,Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.