scholarly journals Pathogen community composition and co-infection patterns in a wild community of rodents

2020 ◽  
Author(s):  
Jessica L. Abbate ◽  
Maxime Galan ◽  
Maria Razzauti ◽  
Tarja Sironen ◽  
Liina Voutilainen ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
Host Species ◽  
Community Sample ◽  
Distribution Patterns ◽  
Amplicon Sequencing ◽  
Transmission Risk ◽  
Cowpox Virus ◽  
Extrinsic Factors ◽  
Rich Diversity

AbstractRodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the incidence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.

scholarly journals Community composition and species richness of parasitoids infesting Yponomeuta species in the Netherlands

2004 ◽  
Vol 73 (4) ◽  
pp. 255-261 ◽  
Author(s):  
Daniel F.R. Cleary
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
The Netherlands ◽  
Community Composition ◽  
Host Species ◽  
Community Similarity ◽  
Parasitoid Species ◽  
Temporal And Spatial Variation ◽  
Significant Difference ◽  
Temporal And Spatial

Parasitoid assemblages infesting Yponomeuta species in the Netherlands were investigated. Parasitoid species richness and community composition were related to host species, habitat, temporal and spatial variation. Both community structure and species richness did not differ among habitats. There was no significant difference in species richness between years (1994 and 1995) but there was a significant difference in community composition. Community composition and species richness both differed among host species, although this latter result was solely due to the host species Y. evonymellus. There was no significant relationship between community similarity and distance. These results indicate that the parasitoids of the moth genus Yponomeuta in the Netherlands appear to form a spatially stable, but temporally variable community. Most of the variation in community structure was, however, related to the host species. The marked difference in parasitoid species richness and community composition of Y. evonymellus when compared to the other species warrants further study.

scholarly journals Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs

2019 ◽  
Vol 95 (12) ◽  
Author(s):  
Zachary S Cooper ◽  
Josephine Z Rapp ◽  
Shelly D Carpenter ◽  
Go Iwahana ◽  
Hajo Eicken ◽  
...  
Keyword(s):  
Community Structure ◽  
Sea Ice ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Extracellular Polysaccharides ◽  
Rrna Gene ◽  
Alpha And Beta Diversity

ABSTRACT Hypersaline aqueous environments at subzero temperatures are known to be inhabited by microorganisms, yet information on community structure in subzero brines is very limited. Near Utqiaġvik, Alaska, we sampled subzero brines (–6°C, 115–140 ppt) from cryopegs, i.e. unfrozen sediments within permafrost that contain relic (late Pleistocene) seawater brine, as well as nearby sea-ice brines to examine microbial community composition and diversity using 16S rRNA gene amplicon sequencing. We also quantified the communities microscopically and assessed environmental parameters as possible determinants of community structure. The cryopeg brines harbored surprisingly dense bacterial communities (up to 108 cells mL–1) and millimolar levels of dissolved and particulate organic matter, extracellular polysaccharides and ammonia. Community composition and diversity differed between the two brine environments by alpha- and beta-diversity indices, with cryopeg brine communities appearing less diverse and dominated by one strain of the genus Marinobacter, also detected in other cold, hypersaline environments, including sea ice. The higher density and trend toward lower diversity in the cryopeg communities suggest that long-term stability and other features of a subzero brine are more important selective forces than in situ temperature or salinity, even when the latter are extreme.

Variation in the components of Benthic community structure in a Coastal Lagoon as a function of Spatial Scale

1989 ◽  
Vol 40 (1) ◽  
pp. 79 ◽  
Author(s):  
A Hatcher
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
Coastal Lagoon ◽  
Benthic Community ◽  
Spatial Scales ◽  
Small Scale ◽  
Benthic Community Structure ◽  
Extrinsic Factors ◽  
Sessile Invertebrates ◽  
Community Types

The perception of community structure is strongly related to the spatial resolution of data collection. To quantify variation in community structure at several spatial scales, the benthos was examined on the limestone substratum in a nearshore coastal lagoon. Community structure was described using a form of pattern analysis called correspondence analysis. Variance at three spatial scales was measured. These scales were described as: (I) between offshore and nearshore reefs (kilometres); (2) among areas on the nearshore reef-line (< 1 km); and (3) between community types on the nearshore reef-line (tens of metres and less). Organisms were classified according to higher taxa/functional classes. Parameters which varied between reef-lines included: (i) community composition determined using multivariate ordination, (ii) cover by calcareous and filamentous algae and (iii) abundance of seagrass and juvenile kelp (Ecklonia radiata). Among the areas on the nearshore reef-line, variance in community composition was due to the distribution of animals. There was a south to north gradient of increasing cover by encrusting animals and abundance of ascidians. Within the areas on the nearshore reef-line, there were two distinct community types characterized by macrophytic plants or sessile invertebrates. The major potential controls of the variation in benthic community structure were different at each of the spatial scales examined. The strong relationships between extrinsic factors and components of the communities suggested that the major potential controls were: (a) exposure to swell at the large scale (between reef-lines), (b) availability of food at the medium scale (within areas on the nearshore reef-line) and (c) biological interactions or responses to microtopography and light climate at the small scale (between and within communities on the nearshore reef-line).

scholarly journals Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau

2016 ◽  
Vol 82 (6) ◽  
pp. 1846-1858 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Li-Li Miao ◽  
Fang Wang ◽  
Li-Min Chu ◽  
...  
Keyword(s):  
Community Structure ◽  
Tibetan Plateau ◽  
Community Composition ◽  
Qaidam Basin ◽  
Nitrogen Concentration ◽  
Distribution Patterns ◽  
The Tibetan Plateau ◽  
Prokaryotic Community ◽  
Content Type ◽  
Ionic Concentrations

ABSTRACTThe prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated byBacteriain lakes with salinities of <100 g/liter and byArchaeain Lake Gasikule. The clades At12OctB3 andSalinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg2+, K+, Cl−, Na+, SO42−, and Ca2+) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO43−concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.

scholarly journals Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

2021 ◽  
Author(s):  
Ya-Jou Chen ◽  
Pok Man Leung ◽  
Jennifer L. Wood ◽  
Sean K. Bay ◽  
Philip Hugenholtz ◽  
...  
Keyword(s):  
Community Composition ◽  
Sulfide Oxidation ◽  
Microbial Community Composition ◽  
Ecological Theory ◽  
Distribution Patterns ◽  
Amplicon Sequencing ◽  
Habitat Disturbance ◽  
Rrna Gene ◽  
Habitat Generalist ◽  
Habitat Generalists

AbstractEcological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.

Dissolved oxygen and temperature best predict deep-sea fish community structure in the Gulf of California with climate change implications

2020 ◽  
Vol 637 ◽  
pp. 159-180
Author(s):  
ND Gallo ◽  
M Beckwith ◽  
CL Wei ◽  
LA Levin ◽  
L Kuhnz ◽  
...  
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Community Composition ◽  
Environmental Conditions ◽  
Deep Sea ◽  
Gulf Of California ◽  
Fish Community ◽  
Demersal Fish ◽  
Fish Community Structure ◽  
Explained Variance

Natural gradient systems can be used to examine the vulnerability of deep-sea communities to climate change. The Gulf of California presents an ideal system for examining relationships between faunal patterns and environmental conditions of deep-sea communities because deep-sea conditions change from warm and oxygen-rich in the north to cold and severely hypoxic in the south. The Monterey Bay Aquarium Research Institute (MBARI) remotely operated vehicle (ROV) ‘Doc Ricketts’ was used to conduct seafloor video transects at depths of ~200-1400 m in the northern, central, and southern Gulf. The community composition, density, and diversity of demersal fish assemblages were compared to environmental conditions. We tested the hypothesis that climate-relevant variables (temperature, oxygen, and primary production) have more explanatory power than static variables (latitude, depth, and benthic substrate) in explaining variation in fish community structure. Temperature best explained variance in density, while oxygen best explained variance in diversity and community composition. Both density and diversity declined with decreasing oxygen, but diversity declined at a higher oxygen threshold (~7 µmol kg-1). Remarkably, high-density fish communities were observed living under suboxic conditions (<5 µmol kg-1). Using an Earth systems global climate model forced under an RCP8.5 scenario, we found that by 2081-2100, the entire Gulf of California seafloor is expected to experience a mean temperature increase of 1.08 ± 1.07°C and modest deoxygenation. The projected changes in temperature and oxygen are expected to be accompanied by reduced diversity and related changes in deep-sea demersal fish communities.

Levels of Spatial Variability: The “Community” Problem

1990 ◽  
Vol 5 ◽  
pp. 13-30 ◽  
Author(s):  
D. A. Springer ◽  
A. I. Miller
Keyword(s):  
Community Structure ◽  
Spatial Variability ◽  
Species Distribution ◽  
Distribution Patterns ◽  
The Past ◽  
Structure And Dynamics ◽  
Evolutionary Units ◽  
The Way

The way we view species distribution patterns, particularly at the level commonly referred to as the “community”, has changed over the past 70 years in biology and, subsequently, in paleontology. Because the degree to which species associations can be interpreted as ecological and evolutionary units depends ultimately on recognition and interpretation of faunal spatial variability, we need to understand the nature of this variability at all levels of resolution before we can adequately address questions of “community” structure and dynamics. While it is possible to recognize spatial variability at several levels, from the distributions of individuals within a species to the overall pattern created by the global biota, we must ask whether these patterns really comprise a hierarchy with natural discontinuities (Fig. 1), or whether it is more realistic to view them as a continuous variability spectrum.

scholarly journals Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?

2021 ◽  
Author(s):  
Tamara J. H. M. van Bergen ◽  
Ana B. Rios-Miguel ◽  
Tom M. Nolte ◽  
Ad M. J. Ragas ◽  
Rosalie van Zelm ◽  
...  
Keyword(s):  
Microbial Community ◽  
Activated Sludge ◽  
Community Composition ◽  
Rate Constants ◽  
Wastewater Treatment Plants ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Initial Concentration ◽  
Different Seasons

Abstract Pharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs). Biotransformation plays an important role in mitigating environmental risks; however, a mechanistic understanding of involved processes is limited. The aim of this study was to evaluate potential relationships between first-order biotransformation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from WWTP Groesbeek (The Netherlands) of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC–MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing, and kb values were calculated. The biodegradable pharmaceuticals were acetaminophen, metformin, metoprolol, terbutaline, and phenazone (ranked from high to low biotransformation rates). Carbamazepine, diatrizoic acid, diclofenac, and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum, different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetic theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP. Key points • Biotransformation and sorption of pharmaceuticals were assessed in activated sludge. • Higher initial concentrations resulted in higher biotransformation rate constants for biodegradable pharmaceuticals. • Summer and winter inocula produced slightly different biotransformation rate constants although microbial community composition did not significantly change. Graphical abstract

A Micro-Community Structure Merging Model Using a Community Sample Matrix

2013 ◽  
Vol 30 (1) ◽  
pp. 018901
Author(s):  
Lin Li ◽  
Hao Peng ◽  
Song-Nian Lu ◽  
Ying Tian
Keyword(s):  
Community Structure ◽  
Community Sample ◽  
Sample Matrix

Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities, and prokaryotic community profiles in Argentinean semi-arid soils

2021 ◽  
Author(s):  
L A Gabbarini ◽  
E Figuerola ◽  
J P Frene ◽  
N B Robledo ◽  
F M Ibarbalz ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Structure ◽  
Management Practices ◽  
Soil Health ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Prokaryotic Community ◽  
C Cycle

Abstract The effects of tillage on soil structure, physiology, and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs. no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles, and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analysed at two soil depths (0–5, 5–10 cm) in samples taken 6, 18, and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils thirty months after switching from CT to NT. Bacteria and Archaea OTUs, which responded to NT were associated with coarse soil fraction, SOC and C cycle enzymes while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.

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