Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi

AbstractBackgroundRepresentatives of the phylum Chloroflexi, though reportedly highly abundant (up to 30% of total prokaryotes) in the extensive deep water habitats of both marine (SAR202) and freshwater (CL500-11), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.ResultsHere we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion specific SL56 cluster. Cell volume analyses show that the CL500-11 are amongst the largest prokaryotic cells in the water column of deep lakes and with a biomass:abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.ConclusionsExtending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.

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Ant Species Diversity, Distribution, and Community Composition in Different Forest Types in Papua New Guinea

Case Studies in the Environment ◽

10.1525/cse.2021.1342727 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Jacob Yombai ◽

Petr Klimes ◽

Paul Dargusch ◽

Aloysius Posman ◽

Ondrej Mottl ◽

...

Keyword(s):

Species Richness ◽

Species Diversity ◽

Sea Level ◽

Papua New Guinea ◽

Community Composition ◽

Scientific Information ◽

New Guinea ◽

Sampling Effort ◽

Forest Types ◽

The Impact

Previous studies have provided important scientific information on ant species richness and composition relating to the effects of elevation, sampling approaches, stratification, and forest succession. Yet, they have primarily focused on single sites or regions. Knowledge of ant ecology should also include the impact of disturbance in various forest types. Tuna baiting and hand collection methods were used to investigate diversity and community composition of ants in 16 sites sampled across Papua New Guinea, in both disturbed and pristine forest, at heights ranging from 28 to 2,728 m above sea level. We found 176 species as a result of exposing 320 tuna baits and traversing 72 hand-searched plots. Baiting samples were strongly dominated by a few common species, while the hand-collecting captured more species per plot. The Chao 2 richness estimator for both methods predicted undersampling of the local community. As expected, ant species diversity and richness significantly decrease with increasing elevation. We observed, on average, greater species diversity of ground-dwelling ant communities in disturbed compared to undisturbed forests. The effect was not significant using multivariate randomisations, since the same species dominated both forest classes. The unexpected pattern of ant species richness being locally higher in the disturbed sites is driven by our sampling of undisturbed communities at all elevations, but sampling of the disturbed communities only up to 1,600 m above sea level. Hence, future studies should consider more locations, aiming ideally for an equal sampling effort to capture disturbance stage and elevation.

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Tree Species Diversity, Composition and Aboveground Biomass Across Dry Forest Land-Cover Types in Coastal Ecuador

Tropical Conservation Science ◽

10.1177/1940082921995415 ◽

2021 ◽

Vol 14 ◽

pp. 194008292199541

Author(s):

Xavier Haro-Carrión ◽

Bette Loiselle ◽

Francis E. Putz

Keyword(s):

Species Diversity ◽

Land Cover ◽

Community Composition ◽

Aboveground Biomass ◽

Tree Species ◽

Dry Forest ◽

Stem Density ◽

Tree Species Diversity ◽

Land Cover Types ◽

Schizolobium Parahyba

Tropical dry forests (TDF) are highly threatened ecosystems that are often fragmented due to land-cover change. Using plot inventories, we analyzed tree species diversity, community composition and aboveground biomass patterns across mature (MF) and secondary forests of about 25 years since cattle ranching ceased (SF), 10–20-year-old plantations (PL), and pastures in a TDF landscape in Ecuador. Tree diversity was highest in MF followed by SF, pastures and PL, but many endemic and endangered species occurred in both MF and SF, which demonstrates the importance of SF for species conservation. Stem density was higher in PL, followed by SF, MF and pastures. Community composition differed between MF and SF due to the presence of different specialist species. Some SF specialists also occurred in pastures, and all species found in pastures were also recorded in SF indicating a resemblance between these two land-cover types even after 25 years of succession. Aboveground biomass was highest in MF, but SF and Tectona grandis PL exhibited similar numbers followed by Schizolobium parahyba PL, Ochroma pyramidale PL and pastures. These findings indicate that although species-poor, some PL equal or surpass SF in aboveground biomass, which highlights the critical importance of incorporating biodiversity, among other ecosystem services, to carbon sequestration initiatives. This research contributes to understanding biodiversity conservation across a mosaic of land-cover types in a TDF landscape.

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Stand structure, community composition and tree species diversity of sub-tropical forest of Nagaland, Northeast India

Tropical Ecology ◽

10.1007/s42965-021-00170-5 ◽

2021 ◽

Author(s):

Aosanen Ao ◽

Sapu Changkija ◽

S. K. Tripathi

Keyword(s):

Species Diversity ◽

Tropical Forest ◽

Community Composition ◽

Tree Species ◽

Stand Structure ◽

Northeast India ◽

Tree Species Diversity ◽

Structure Community

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Are Bacterio- and Phytoplankton Community Compositions Related in Lakes Differing in Their Cyanobacteria Contribution and Physico-Chemical Properties?

Genes ◽

10.3390/genes12060855 ◽

2021 ◽

Vol 12 (6) ◽

pp. 855

Author(s):

Mikołaj Kokociński ◽

Dariusz Dziga ◽

Adam Antosiak ◽

Janne Soininen

Keyword(s):

Environmental Factors ◽

Community Composition ◽

Phytoplankton Community ◽

Heterotrophic Bacteria ◽

Bacterial Community Composition ◽

Physical Factors ◽

Research Attention ◽

Phytoplankton Community Composition ◽

The Impact ◽

Bacteria Communities

Bacterioplankton community composition has become the center of research attention in recent years. Bacteria associated with toxic cyanobacteria blooms have attracted considerable interest. However, little is known about the environmental factors driving the bacteria community, including the impact of invasive cyanobacteria. Therefore, our aim has been to determine the relationships between heterotrophic bacteria and phytoplankton community composition across 24 Polish lakes with different contributions of cyanobacteria including the invasive species Raphidiopsis raciborskii. This analysis revealed that cyanobacteria were present in 16 lakes, while R. raciborskii occurred in 14 lakes. Our results show that bacteria communities differed between lakes dominated by cyanobacteria and lakes with minor contributions of cyanobacteria but did not differ between lakes with R. raciborskii and other lakes. Physical factors, including water and Secchi depth, were the major drivers of bacteria and phytoplankton community composition. However, in lakes dominated by cyanobacteria, bacterial community composition was also influenced by biotic factors such as the amount of R. raciborskii, chlorophyll-a and total phytoplankton biomass. Thus, our study provides novel evidence on the influence of environmental factors and R. raciborskii on lake bacteria communities.

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Vegetation Dynamic Assessment by NDVI and Field Observations for Sustainability of China’s Wulagai River Basin

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18052528 ◽

2021 ◽

Vol 18 (5) ◽

pp. 2528

Author(s):

Panpan Chen ◽

Huamin Liu ◽

Zongming Wang ◽

Dehua Mao ◽

Cunzhu Liang ◽

...

Keyword(s):

Species Diversity ◽

River Basin ◽

Vegetation Change ◽

Vegetation Index ◽

Dynamic Assessment ◽

Indicator System ◽

Vegetation Changes ◽

Vegetation Dynamic ◽

Management Policies ◽

The Impact

Accurate monitoring of grassland vegetation dynamics is essential for ecosystem restoration and the implementation of integrated management policies. A lack of information on vegetation changes in the Wulagai River Basin restricts regional development. Therefore, in this study, we integrated remote sensing, meteorological, and field plant community survey data in order to characterize vegetation and ecosystem changes from 1997 to 2018. The residual trend (RESTREND) method was utilized to detect vegetation changes caused by human factors, as well as to evaluate the impact of the management of pastures. Our results reveal that the normalized difference vegetation index (NDVI) of each examined ecosystem type showed an increasing trend, in which anthropogenic impact was the primary driving force of vegetation change. Our field survey confirmed that the meadow steppe ecosystem increased in species diversity and aboveground biomass; however, the typical steppe and riparian wet meadow ecosystems experienced species diversity and biomass degradation, therefore suggesting that an increase in NDVI may not directly reflect ecosystem improvement. Selecting an optimal indicator or indicator system is necessary in order to formulate reasonable grassland management policies for increasing the sustainability of grassland ecosystems.

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Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

Journal of Fungi ◽

10.3390/jof7070565 ◽

2021 ◽

Vol 7 (7) ◽

pp. 565

Author(s):

Anindita Lahiri ◽

Brian R. Murphy ◽

Trevor R. Hodkinson

Keyword(s):

Community Composition ◽

Environmental Effects ◽

High Throughput Sequencing ◽

Fungal Community Composition ◽

Species Identity ◽

Ash Dieback ◽

Hymenoscyphus Fraxineus ◽

Culture Independent ◽

The Impact ◽

Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

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Effects of soil physical characteristics and biotic interferences on the herbaceous community composition and species diversity on the campus of Banaras Hindu University, India

The Environmentalist ◽

10.1007/s10669-010-9276-7 ◽

2010 ◽

Vol 30 (3) ◽

pp. 289-298 ◽

Cited By ~ 7

Author(s):

R. Sagar ◽

Punita Verma

Keyword(s):

Species Diversity ◽

Community Composition ◽

Physical Characteristics ◽

Soil Physical Characteristics ◽

Herbaceous Community

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What is the impact of Impatiens glandulifera on species diversity of invaded riparian vegetation?

Biological Conservation ◽

10.1016/j.biocon.2006.03.025 ◽

2006 ◽

Vol 132 (2) ◽

pp. 143-152 ◽

Cited By ~ 149

Author(s):

Martin Hejda ◽

Petr Pyšek

Keyword(s):

Species Diversity ◽

Riparian Vegetation ◽

Impatiens Glandulifera ◽

The Impact

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Genomic and phenotypic characterisation of invasive neonatal and colonising group B Streptococcus isolates from Slovenia, 2001–2018

BMC Infectious Diseases ◽

10.1186/s12879-020-05599-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Tina Perme ◽

Daniel Golparian ◽

Maja Bombek Ihan ◽

Andrej Rojnik ◽

Miha Lučovnik ◽

...

Keyword(s):

Pregnant Women ◽

Virulence Factors ◽

Late Onset ◽

Group B Streptococcus ◽

Genomic Diversity ◽

Neonatal Disease ◽

Phenotypic Characterisation ◽

High Prevalence ◽

Group B ◽

The Impact

Abstract Background Group B Streptococcus (GBS) is the leading cause of invasive neonatal disease in the industrialized world. We aimed to genomically and phenotypically characterise invasive GBS isolates in Slovenia from 2001 to 2018 and contemporary colonising GBS isolates from screening cultures in 2018. Methods GBS isolates from 101 patients (invasive isolates) and 70 pregnant women (colonising isolates) were analysed. Basic clinical characteristics of the patients were collected from medical records. Antimicrobial susceptibility and phenotypic capsular serotype were determined. Whole-genome sequencing was performed to assign multilocus sequence types (STs), clonal complexes (CCs), pathogenicity/virulence factors, including capsular genotypes, and genome-based phylogeny. Results Among invasive neonatal disease patients, 42.6% (n = 43) were females, 41.5% (n = 39/94) were from preterm deliveries (< 37 weeks gestation), and 41.6% (n = 42) had early-onset disease (EOD). All isolates were susceptible to benzylpenicillin with low minimum inhibitory concentrations (MICs; ≤0.125 mg/L). Overall, 7 serotypes were identified (Ia, Ib, II-V and VIII); serotype III being the most prevalent (59.6%). Twenty-eight MLST STs were detected that clustered into 6 CCs. CC-17 was the most common CC overall (53.2%), as well as among invasive (67.3%) and non-invasive (32.9%) isolates (p < 0.001). CC-17 was more common among patients with late-onset disease (LOD) (81.4%) compared to EOD (47.6%) (p < 0.001). The prevalence of other CCs was 12.9% (CC-23), 11.1% (CC-12), 10.5% (CC-1), 8.2% (CC-19), and 1.8% (CC-498). Of all isolates, 2.3% were singletons. Conclusions A high prevalence of hypervirulent CC-17 isolates, with low genomic diversity and characteristic profile of pathogenicity/virulence factors, was detected among invasive neonatal and colonising GBS isolates from pregnant women in Slovenia. This is the first genomic characterisation of GBS isolates in Slovenia and provides valuable microbiological and genomic baseline data regarding the invasive and colonising GBS population nationally. Continuous genomic surveillance of GBS infections is crucial to analyse the impact of IND prevention strategies on the population structure of GBS locally, nationally, and internationally.

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