scholarly journals Environment drives high phylogenetic turnover among oceanic bacterial communities

2012 ◽  
Vol 8 (4) ◽  
pp. 562-566 ◽  
Author(s):  
Thomas Pommier ◽  
Emmanuel J. P. Douzery ◽  
David Mouillot
Keyword(s):  
Bacterial Communities ◽  
Environmental Gradient ◽  
Regional Scale ◽  
Environmental Filtering ◽  
Species Level ◽  
Geographical Distance ◽  
Abiotic Conditions ◽  
High Connectivity ◽  
Phylogenetic Lineages ◽  
Marine Microbial Communities

Although environmental filtering has been observed to influence the biodiversity patterns of marine bacterial communities, it was restricted to the regional scale and to the species level, leaving the main drivers unknown at large biogeographic scales and higher taxonomic levels. Bacterial communities with different species compositions may nevertheless share phylogenetic lineages, and phylogenetic turnover (PT) among those communities may be surprisingly low along any biogeographic or environmental gradient. Here, we investigated the relative influence of environmental filtering and geographical distance on the PT between marine bacterial communities living more than 8000 km apart in contrasted abiotic conditions. PT was high between communities and was more structured by local environmental factors than by geographical distance, suggesting the predominance of a lineage filtering process. Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities.

scholarly journals Multi-scale comparisons of tree composition in Amazonian terra firme forests

2009 ◽  
Vol 6 (11) ◽  
pp. 2719-2731 ◽  
Author(s):  
E. N. Honorio Coronado ◽  
T. R. Baker ◽  
O. L. Phillips ◽  
N. C. A. Pitman ◽  
R. T. Pennington ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Soil Fertility ◽  
Regional Scale ◽  
Floristic Composition ◽  
Species Level ◽  
Geographical Distance ◽  
Terra Firme ◽  
Floristic Similarity ◽  
North Western ◽  
Scale Variation

Abstract. We explored the floristic composition of terra firme forests across Amazonia using 55 plots. Firstly, we examined the floristic patterns using both genus- and species-level data and found that the species-level analysis more clearly distinguishes among forests. Next, we compared the variation in plot floristic composition at regional- and continental-scales, and found that average among-pair floristic similarity and its decay with distance behave similarly at regional- and continental-scales. Nevertheless, geographical distance had different effects on floristic similarity within regions at distances <100 km, where north-western and south-western Amazonian regions showed greater floristic variation than plots of central and eastern Amazonia. Finally, we quantified the role of environmental factors and geographical distance for determining variation in floristic composition. A partial Mantel test indicated that while geographical distance appeared to be more important at continental scales, soil fertility was crucial at regional scales within western Amazonia, where areas with similar soil conditions were more likely to share a high number of species. Overall, these results suggest that regional-scale variation in floristic composition can rival continental-scale differences within Amazonian terra firme forests, and that variation in floristic composition at both scales is influenced by geographical distance and environmental factors, such as climate and soil fertility. To fully account for regional-scale variation in continental studies of floristic composition, future floristic studies should focus on forest types poorly represented at regional scales in current datasets, such as terra firme forests with high soil fertility in north-western Amazonia.

scholarly journals Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Christian Milani ◽  
Giulia Alessandri ◽  
Marta Mangifesta ◽  
Leonardo Mancabelli ◽  
Gabriele Andrea Lugli ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Cost Effective ◽  
Species Level ◽  
Clinical Settings ◽  
Mucosal Biopsy ◽  
Environmental Matrices ◽  
Novel Biomarkers ◽  
Bacterial Profiling

ABSTRACT 16S small-subunit (SSU) rRNA gene-based bacterial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to the genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a bacterial profiling method based on the internal transcribed spacer (ITS) region employing optimized primers and a comprehensive ITS database for accurate cataloguing of bacterial communities at (sub)species resolution. Performance of the microbial ITS profiling pipeline was tested through analysis of host-associated, food, and environmental matrices, while its efficacy in clinical settings was assessed through analysis of mucosal biopsy specimens of colorectal cancer, leading to the identification of putative novel biomarkers. The data collected indicate that the proposed pipeline represents a major step forward in cost-effective identification and screening of microbial biomarkers at (sub)species level, with relevant impact in research, industrial, and clinical settings. IMPORTANCE We developed a novel method for accurate cataloguing of bacterial communities at (sub)species level involving amplification of the internal transcribed spacer (ITS) region through optimized primers, followed by next-generation sequencing and taxonomic classification of amplicons by means of a comprehensive database of bacterial ITS sequences. Host-associated, food, and environmental matrices were employed to test the performance of the microbial ITS profiling pipeline. Moreover, mucosal biopsy samples from colorectal cancer patients were analyzed to demonstrate the scientific relevance of this profiling approach in a clinical setting through identification of putative novel biomarkers. The results indicate that the ITS-based profiling pipeline proposed here represents a key metagenomic tool with major relevance for research, industrial, and clinical settings.

scholarly journals Identifying the Drivers of Spatial Taxonomic and Functional Beta-Diversity of British Breeding Birds

2021 ◽  
Vol 9 ◽  
Author(s):  
Joseph P. Wayman ◽  
Jonathan P. Sadler ◽  
Thomas A. M. Pugh ◽  
Thomas E. Martin ◽  
Joseph A. Tobias ◽  
...  
Keyword(s):  
Land Use ◽  
Beta Diversity ◽  
Environmental Filtering ◽  
Bird Species ◽  
Predictor Variable ◽  
Dispersal Limitation ◽  
Functional Change ◽  
Pairwise Distance ◽  
Geographical Distance ◽  
Human Influence

Spatial variation in community composition may be driven by a variety of processes, including environmental filtering and dispersal limitation. While work has been conducted on the relative importance of these processes on various taxa and at varying resolutions, tests using high-resolution empirical data across large spatial extents are sparse. Here, we use a dataset on the presence/absence of breeding bird species collected at the 10 km × 10 km scale across the whole of Britain. Pairwise spatial taxonomic and functional beta diversity, and the constituent components of each (turnover and nestedness/richness loss or gain), were calculated alongside two other measures of functional change (mean nearest taxon distance and mean pairwise distance). Predictor variables included climate and land use measures, as well as a measure of elevation, human influence, and habitat diversity. Generalized dissimilarity modeling was used to analyze the contribution of each predictor variable to variation in the different beta diversity metrics. Overall, we found that there was a moderate and unique proportion of the variance explained by geographical distance per se, which could highlight the role of dispersal limitation in community dissimilarity. Climate, land use, and human influence all also contributed to the observed patterns, but a large proportion of the explained variance in beta diversity was shared between these variables and geographical distance. However, both taxonomic nestedness and functional nestedness were uniquely predicted by a combination of land use, human influence, elevation, and climate variables, indicating a key role for environmental filtering. These findings may have important conservation implications in the face of a warming climate and future land use change.

scholarly journals Roads as conduits of taxonomic, functional and phylogenetic degradation in caatinga vegetation

2020 ◽  
Author(s):  
Nayara Mesquita Mota ◽  
Markus Gastauer ◽  
Juan Fernando Carrión ◽  
João Augusto Alves Meira-Neto
Keyword(s):  
Plant Communities ◽  
Phylogenetic Diversity ◽  
Plant Traits ◽  
Environmental Filtering ◽  
Maximum Diameter ◽  
Maximum Height ◽  
Phylogenetic Structure ◽  
Caatinga Vegetation ◽  
Phylogenetic Lineages ◽  
Functional And Phylogenetic Diversity

AbstractRoad networks cause disturbances that can alter the biodiversity and the functioning of the Caatinga ecosystems. We tested the hypotheses that (i) Caatinga vegetation near roads is less taxonomically, functionally and phylogenetically diverse, (ii) phylogenetically and functionally more clustered than vegetation further from roads, (iii) plant traits associated with herbivory deterrence are conserved within the phylogenetic lineages, and (iv) Caatinga vegetation near roads selects for disturbance-related traits. We sampled herbaceous and woody component of vegetation in four plots near roads and four plots further from roads to test these hypothesis. Sampled species were classified according to their resprouting capacity, nitrogen fixation, succulence/spines, urticancy/toxicity, lifeform, endozoochory, maximum height and maximum diameter, before we calculated the taxonomic, functional and phylogenetic diversity of plant communities. Species richness, taxonomic, functional and phylogenetic diversities were lower in plots close to the roads, confirming roads as sources of disturbances. The phylogenetic structure of the Caatinga vegetation near roads was clustered, indicating environmental filtering by herbivory as the main pervasive disturbance in Caatinga ecosystems, since traits related to herbivory deterrence were conserved within phylogenetic lineages and were filtered in near roads. Thus, roads should be considered degradation conduits causing taxonomic, phylogenetic and functional impoverishment of Caatinga vegetation.

scholarly journals Coexistence patterns and diversity in a trait-based metacommunity on an environmental gradient

2022 ◽  
Author(s):  
Mozzamil Mohammed ◽  
Bernd Blasius ◽  
Alexey Ryabov
Keyword(s):  
Environmental Gradient ◽  
Environmental Variability ◽  
Environmental Filtering ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Spatially Explicit Model ◽  
Regional Diversity ◽  
Local Species Richness ◽  
Local Species ◽  
Source Sink

AbstractThe dynamics of trait-based metacommunities have attracted much attention, but not much is known about how dispersal and spatial environmental variability mutually interact with each other to drive coexistence patterns and diversity. Here, we present a spatially explicit model of competition for two essential resources in a metacommunity on a one-dimensional environmental gradient. We find that both the strength of dispersal and the range of spatial environmental variability affect coexistence patterns, spatial structure, trait distribution, and local and regional diversity. Without dispersal, species are sorted according to their optimal growth conditions on the gradient. With the onset of dispersal, source-sink effects are initiated, which increases the effects of environmental filtering and interspecific competition and generates trait lumping, so that only a few species from an environment-defined trait range can survive. Interestingly, for very large dispersal rates, species distributions become spatially homogeneous, but nevertheless two species at the extreme ends of the trade-off curve can coexist for large environmental variability. Local species richness follows a classic hump-shaped dependence on dispersal rate, while local and regional diversity exhibit a pronounced peak for intermediate values of the environmental variability. Our findings provide important insights into the factors that shape the structure of trait-based metacommunities.

Turnover is replaced by nestedness with increasing geographical distance in bacterial communities of coastal shallow lakes

2020 ◽  
Vol 71 (9) ◽  
pp. 1086
Author(s):  
Marla Sonaira Lima ◽  
Fabiana Schneck ◽  
Ng Haig They ◽  
Luciane Oliveira Crossetti ◽  
Juliana Elisa Bohnenberger ◽  
...  
Keyword(s):  
Shallow Lakes ◽  
Bacterial Communities ◽  
Local Environment ◽  
Dispersal Limitation ◽  
Geographical Distance ◽  
Environmental Filters ◽  
Species Sorting ◽  
Relative Contribution ◽  
Β Diversity ◽  
The Relationship

In this study we measured the relative contribution of two components of β-diversity, turnover and nestedness, of bacterioplankton among 25 shallow lakes in southern Brazil and tested their relationship with local (environment, chlorophyll-a and biomass of phytoplanktonic classes) and landscape variables, as well as geographical distance. We predicted that turnover would be the largest share of total β-diversity due to the variation of local characteristics among lakes. Further, we expected nestedness to increase at the expense of turnover with increasing geographical distance among lakes due to dispersal limitation. The results indicated a higher contribution of turnover than nestedness to total β-diversity, which was driven by local factors. When the relationship between β-diversity components and the spatial extent between each lake and all other lakes was considered, turnover was replaced by nestedness with increasing geographical distance for 8 (the furthermost lakes) of the 25 lakes likely because of a combination of decreasing dispersal due to distance and richness differences due to wind-driven mass effects. The results of this study suggest a role for nestedness as an indicator of dispersal limitation owing to geographical distance and wind dispersal, and for turnover as an indicator of species sorting because of environmental filters for these freshwater bacterial communities.

Heterochrony and Phylogenetic Trends

Paleobiology ◽  
1982 ◽  
Vol 8 (2) ◽  
pp. 130-142 ◽  
Author(s):  
Kenneth J. McNamara
Keyword(s):  
Environmental Gradient ◽  
Morphological Evolution ◽  
Species Level ◽  
Genetic Isolation ◽  
Punctuated Equilibria ◽  
Morphological Gradient ◽  
Morphological Stasis ◽  
Species Establishment ◽  
Morphological Novelties ◽  
Selection Of

A model is proposed, based on examples that have been interpreted as phylogenetic trends, to explain how directional morphological evolution at the species level can arise by heterochrony. The examples illustrated are of Tertiary to Recent rhynchonellide brachiopods, Cambrian olenellid trilobites, living spatangoid echinoids, Tertiary to Recent schizasterid echinoids, Cenomanian ammonites and Silurian monograptids. Morphological discontinuities between species along morphological gradients (which can be recognised both spatially and/or temporally), and temporal morphological stasis within species, are both consistent with the punctuated equilibria model of macroevolution. It is argued that morphological discontinuities have arisen by selection of morphological novelties produced by heterochronic processes. These novelties are preadaptations which allow ecological and, consequently, genetic isolation from ancestral species. Establishment of a heterochronic morphological gradient is only possible given a suitable environmental gradient. The terms “paedomorphocline” and “peramorphocline” are proposed for these heterochronic morphological gradients. Paedomorphoclines and peramorphoclines each comprise a number of species occupying a series of adaptive peaks, which have evolved sequentially through time by selection along an environmental gradient.

scholarly journals Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils

2006 ◽  
Vol 72 (11) ◽  
pp. 6965-6971 ◽  
Author(s):  
David K. Oline
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Regional Scale ◽  
Serpentine Soils ◽  
Operational Taxonomic Units ◽  
Microbial Biogeography ◽  
Soil Bacterial Communities ◽  
Culture Independent ◽  
Control Community ◽  
16S Rrna Clone Libraries

ABSTRACT I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

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