Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans

Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute toward gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.

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Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652031 ◽

2021 ◽

Vol 12 ◽

Author(s):

Matteo Daghio ◽

Francesca Ciucci ◽

Arianna Buccioni ◽

Alice Cappucci ◽

Laura Casarosa ◽

...

Keyword(s):

Bacterial Community ◽

Growth Performance ◽

Community Composition ◽

Lipid Composition ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Daily Weight Gain ◽

Rrna Gene ◽

Rumen Microbiota ◽

Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

Frontiers in Microbiology ◽

10.3389/fmicb.2020.626713 ◽

2021 ◽

Vol 11 ◽

Author(s):

Janneke Schreuder ◽

Francisca C. Velkers ◽

Alex Bossers ◽

Ruth J. Bouwstra ◽

Willem F. de Boer ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Intestinal Microbiota ◽

Environmental Changes ◽

Temporal Dynamics ◽

Microbial Community Composition ◽

Sudden Change ◽

Rrna Gene ◽

Poultry House ◽

Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

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Gut microbiome composition predicts summer core range size in two divergent ungulates

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab048 ◽

2021 ◽

Vol 97 (5) ◽

Author(s):

Jesse F Wolf ◽

Krystal D Kriss ◽

Kara M MacAulay ◽

Keith Munro ◽

Brent R Patterson ◽

...

Keyword(s):

Habitat Use ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Research Question ◽

Negative Relationship ◽

Range Size ◽

Feeding Strategies ◽

Rrna Gene ◽

Home Ranges ◽

Mountain Goats

ABSTRACT The gut microbiome of animals vary by age, diet, and habitat, and directly influences an individual's health. Similarly, variation in home ranges is linked to feeding strategies and fitness. Ungulates (hooved mammals) exhibit species-specific microbiomes and habitat use patterns. We combined gut microbiome and movement data to assess relationships between space use and the gut microbiome in a specialist and a generalist ungulate. We GPS radiocollared 24 mountain goats (Oreamnos americanus) and 34 white-tailed deer (Odocoileus virginianus), collected fecal samples, and conducted high-throughput sequencing of the 16S rRNA gene. We generated gut diversity metrics and key bacterial ratios. Our research question centred around the idea that larger Firmicutes to Bacteroidetes ratios confer body size or fat advantages that allow for larger home ranges, and relationships of disproportionate habitat use are stronger in the habitat specialist mountain goat. Firmicutes to Bacteroidetes ratios were positively correlated with core range area in both species. Mountain goats exhibited a negative relationship between gut diversity and proportional use of treed areas and escape terrain, and no relationships were detected in the habitat generalist white-tailed deer. This is the first study to relate range size to the gut microbiome in wild ungulates and is an important proof of concept that advances the information that can be gleaned from non-invasive sampling.

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Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

Microbial Ecology ◽

10.1007/s00248-021-01763-2 ◽

2021 ◽

Author(s):

Jun Zhao ◽

Baozhan Wang ◽

Xue Zhou ◽

Mohammad Saiful Alam ◽

Jianbo Fan ◽

...

Keyword(s):

Community Composition ◽

High Throughput Sequencing ◽

Environmental Changes ◽

Agricultural Soils ◽

Terrestrial Ecosystems ◽

Low Ph ◽

Ph Change ◽

Monooxygenase Gene ◽

Ammonia Oxidising Archaea

AbstractAmmonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.

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Phylogenetic Ecology of the Freshwater Actinobacteria acI Lineage

Applied and Environmental Microbiology ◽

10.1128/aem.00794-07 ◽

2007 ◽

Vol 73 (22) ◽

pp. 7169-7176 ◽

Cited By ~ 141

Author(s):

Ryan J. Newton ◽

Stuart E. Jones ◽

Matthew R. Helmus ◽

Katherine D. McMahon

Keyword(s):

16S Rrna ◽

Community Composition ◽

Strong Predictor ◽

Regional Scale ◽

16S Rrna Genes ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Data Set ◽

Biogeographic Patterns

ABSTRACT The acI lineage of freshwater Actinobacteria is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions from 18 Wisconsin lakes and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local scale (within lakes) and at the regional scale (across lakes). Phylogenetic reconstruction of 434 acI 16S rRNA genes revealed a well-defined and highly resolved phylogeny. Eleven previously unrecognized monophyletic clades, each with ≥97.9% within-clade 16S rRNA gene sequence identity, were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that the lakes represent a single biotic region containing environmental filters for communities that have similar compositions. Phylogenetically disparate clades within the acI lineage were most abundant at the regional scale, and local communities were comprised of more closely related clades. Lake pH was a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the data set. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The nonrandom distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with acI clades AI, BII, and BIII preferring acidic lakes and acI clades AII, AVI, and BI preferring more alkaline lakes.

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Vergleichende Analysen des Lungenmikrobioms zwischen Patienten mit ANCA-assoziierten Vaskulitiden und Sarkoidose aus bronchoalveolärer Lavage

Karger Kompass Autoimmun ◽

10.1159/000511745 ◽

2020 ◽

Vol 2 (4) ◽

pp. 165-166

Author(s):

Nicolas Carlos Kahn

Keyword(s):

High Throughput Sequencing ◽

Smoking Status ◽

Bacterial Community Composition ◽

Negative Relationship ◽

Human Microbiome ◽

P Value ◽

Rrna Gene ◽

Oral Microbiota ◽

Α Diversity ◽

The Difference

Microbial involvement in the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, both of which have lung involvement. However, exhaustive research to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed. We sought to elucidate the distinct dysbiotic lung microbiota between AAV and sarcoidosis. We used 16S rRNA gene high-throughput sequencing to obtain the bacterial community composition of bronchoalveolar lavage fluid (BALF) in patients with AAV (n = 16) compared to patients with sarcoidosis (n = 21). The patients had not undergone therapy with immunosuppressive medication when their BALF was acquired. No difference was observed in α-diversity between patients with AAV and patients with sarcoidosis when using all the detected taxa. We defined the taxa of the oral cavity by using the data of oral microbiota of healthy individuals from the Human Microbiome Project (HMP). The analysis using only oral taxa made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. Besides, the analysis using detected taxa except for oral taxa also made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. A linear negative relationship between the α-diversity and Birmingham vasculitis activity score (BVAS) was detected in the AAV group. The observed p-value for the effect of the disease groups on the ß-diversity was small while the effect of other factors including sex and smoking status did not have small p-values. By excluding oral taxa from all the detected taxa, we found a cluster mainly consisted of sarcoidosis patients which was characterized with microbial community monopolized by Erythrobacteraceae family. Our results suggested the importance of considering the influence of oral microbiota in evaluating lung microbiota.

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Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe

Scientific Reports ◽

10.1038/srep23488 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 30

Author(s):

Jing Zhang ◽

Fang Wang ◽

Rongxiao Che ◽

Ping Wang ◽

Hanke Liu ◽

...

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Community Composition ◽

Plant Species ◽

Mycorrhizal Fungi ◽

Environmental Changes ◽

Regional Scale ◽

Arbuscular Mycorrhizal ◽

Future Climate Change ◽

Alpine Steppe ◽

Amf Communities

Abstract Tibetan Plateau is one of the largest and most unique habitats for organisms including arbuscular mycorrhizal fungi (AMF). However, it remains unclear how AMF communities respond to key environmental changes in this harsh environment. To test if precipitation could be a driving force in shaping AMF community structures at regional scale, we examined AMF communities associated with dominant plant species along a precipitation gradient in Tibetan alpine steppe. Rhizosphere soils were collected from five sites with annual precipitation decreasing from 400 to 50 mm. A total of 31 AMF operational taxonomic units (OTUs) were identified. AMF community composition varied significantly among sites, whereas AMF community composition did not vary among plant species. Path analysis revealed that precipitation directly affected AMF hyphal length density, and indirectly influenced AMF species richness likely through the mediation of plant coverage. Our results suggested that water availability could drive the changes of AMF communities at regional scale. Given the important roles AMF could play in the dynamics of plant communities, exploring the changes of AMF communities along key environmental gradients would help us better predict the ecosystem level responses of the Tibetan vegetation to future climate change.

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Vergleichende Analysen des Lungenmikrobioms zwischen Patienten mit ANCA-assoziierten Vaskulitiden und Sarkoidose aus bronchoalveolärer Lavage

Karger Kompass Pneumologie ◽

10.1159/000512607 ◽

2020 ◽

pp. 1-2

Author(s):

Nicolas Carlos Kahn

Keyword(s):

High Throughput Sequencing ◽

Smoking Status ◽

Bacterial Community Composition ◽

Negative Relationship ◽

Human Microbiome ◽

P Value ◽

Rrna Gene ◽

Oral Microbiota ◽

Α Diversity ◽

The Difference

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Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities

ARPHA Conference Abstracts ◽

10.3897/aca.4.e64972 ◽

2021 ◽

Vol 4 ◽

Author(s):

Kristiina Vuorio ◽

Anita Mäki ◽

Pauliina Salmi ◽

Sanni Aalto ◽

Marja Tiirola ◽

...

Keyword(s):

Community Composition ◽

High Throughput ◽

Copy Number ◽

High Throughput Sequencing ◽

Ecological Status ◽

Boreal Lakes ◽

Reliable Estimate ◽

Rrna Gene ◽

Eukaryotic Phytoplankton ◽

Phytoplankton Communities

Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation in the copy number of the rRNA gene between phytoplankton species (Mäki et al. 2017). On the contrary, RNA is present only in living organisms and reflects active protein synthesis. Therefore, RNA-based methods can provide a more reliable estimate of community composition. The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of cyanobacterial and eukaryotic phytoplankton genes hinder the application of DNA-based molecular methods. We applied a directional random-primed high throughput sequencing (HTS) approach (Mäki and Tiirola 2018) to analyse 16S and 18S rRNA community structures of 83 boreal lakes in Finland, Northern Europe. With the method it was possible to simultaneously amplify all groups of aquatic microorganisms in addition to cyanobacteria and eukaryotic phytoplankton. A comparison between microscopy and HTS showed that the relative phylum (Fig. 0) and class level abundances of eukaryotic phytoplankton and order level abundances of cyanobacteria were consistent between the methods, despite that the HTS method overestimated the relative abundance of cyanobacteria. However, correspondence was low at genus and species level, mainly due to the lack of reference library sequences. HTS revealed more genera and was able to differentiate cryptic genera lacking morphological characteristics, but microscopy revealed a longer list of species (Vuorio et al. 2020). The RNA-based method applied showed potential, but it is not yet able to replace microscopy, mainly due to the lack of full length 16S and 18S sequences in the reference libraries. The main advantage of the method is that it is not limited to phytoplankton, but can be applied to simultaneous investigation of the total composition of microbes, including all bacteria, protists, ciliates, rotifers and zooplankton.

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Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

Microorganisms ◽

10.3390/microorganisms8020311 ◽

2020 ◽

Vol 8 (2) ◽

pp. 311

Author(s):

Xin Tai ◽

Rui Li ◽

Bao Zhang ◽

Hao Yu ◽

Xiao Kong ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Community Assembly ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Sediment Samples ◽

Pollution Levels ◽

Water And Sediment

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.

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