Physicochemical and biological dynamics in a coastal Antarctic lake as it transitions from frozen to open water

AbstractPony Lake, at Cape Royds, Antarctica, is a shallow, eutrophic, coastal lake that freezes solid in the winter. Changes in Pony Lake's physicochemical parameters and microbial community were studied during the transition from ice to open water. Due to rising water temperatures, the progressive melt of the ice column and the gradual mixing of basal brines into the remaining water column, Pony Lake evolved physically and chemically over the course of the summer, thereby affecting the microbial community composition. Temperature, pH, conductivity, nutrients and major ion concentrations reached their maximum in January. Pony Lake was colonized by bacteria, viruses, phytoflagellates, ciliates, and a small number of rotifers. Primary and bacterial production were highest in mid-December (2.66 mg C l-1d-1and 30.5 μg C l-1d-1, respectively). A 16S rRNA gene analysis of the bacterioplankton revealed 34 unique sequences dominated by members of theβ- andγ-proteobacterialineages. Cluster analyses on denaturing gradient gel electrophoresis (DGGE) banding patterns and community structure indicated a shift in the dominant members of the microbial community during the transition from winter ice, to early, and late summer lakewater. Our data demonstrate that temporal changes in physicochemical parameters during the summer months determine community dynamics and mediate changes in microbial species composition.

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Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta

Microorganisms ◽

10.3390/microorganisms8081181 ◽

2020 ◽

Vol 8 (8) ◽

pp. 1181

Author(s):

Reynaldo Núñez Salazar ◽

Carlos Aguirre ◽

Jorge Soto ◽

Pamela Salinas ◽

Carlos Salinas ◽

...

Keyword(s):

Microbial Community ◽

High Altitude ◽

Water Column ◽

Physicochemical Parameters ◽

Microbial Community Composition ◽

Atacama Desert ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Lake System ◽

Influence Of Water

Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.

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Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

SOIL ◽

10.5194/soil-2-487-2016 ◽

2016 ◽

Vol 2 (3) ◽

pp. 487-498 ◽

Cited By ~ 13

Author(s):

Belinda C. Martin ◽

Suman J. George ◽

Charles A. Price ◽

Esmaeil Shahsavari ◽

Andrew S. Ball ◽

...

Keyword(s):

Microbial Community ◽

Microbial Activity ◽

Community Dynamics ◽

Denaturing Gradient Gel Electrophoresis ◽

Plant Root ◽

Root Exudation ◽

Microbial Community Composition ◽

Gas Chromatography Mass Spectrometry ◽

Potential Implication ◽

Microbial Community Dynamics

Abstract. Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg−1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g−1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography–mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

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Effect of Nutrient Periodicity on Microbial Community Dynamics

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3175-3183.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3175-3183 ◽

Cited By ~ 35

Author(s):

Militza Carrero-Colï¿½n ◽

Cindy H. Nakatsu ◽

Allan Konopka

Keyword(s):

Community Structure ◽

Microbial Community ◽

Growth Rates ◽

Community Dynamics ◽

Denaturing Gradient Gel Electrophoresis ◽

Pulse Interval ◽

Substrate Affinity ◽

Rrna Gene ◽

Similarity Coefficients ◽

Microbial Community Dynamics

ABSTRACT When microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. This hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. Growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h−1 to 0.15 h−1 as the pulse interval increased from 1 to 14 days. The dynamics of community structure were monitored by 16S rRNA gene PCR-denaturing gradient gel electrophoresis. At pulse intervals of more than 1 day, the community composition continued to change over 130 days. Although replicate systems exposed to the same pulse interval were physiologically similar, their community compositions could exhibit as much dissimilarity (Dice similarity coefficients of <0.5) as did systems operated at different intervals. Bacteria were cultivated from the systems to determine if the physiological characteristics of individual members were consistent with the measured performance of the systems. The isolates fell into three bacterial divisions, Bacteroidetes, Proteobacteria, and Actinobacteria. In agreement with community results, bacteria isolated from systems pulsed every day with nutrients had higher growth rates and ectoaminopeptidase specific activities than isolates from systems pulsed every 14 days. However, the latter isolates did not survive starvation longer than those provided with nutrients every day. The present study demonstrates the dynamic nature of microbial communities exposed to even simple and regular environmental discontinuities when a substantial pool of species that can catabolize the limiting substrate is present.

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Influence of the Depth and Season on Microbial Community Dynamics of the Black Sea

10.21203/rs.3.rs-693853/v1 ◽

2021 ◽

Author(s):

Rafet Cagri Ozturk ◽

Ilhan Altinok ◽

Ali Muzaffer Feyzioglu ◽

Erol Capkin ◽

Ilknur Yildiz

Keyword(s):

Microbial Community ◽

Community Composition ◽

Black Sea ◽

Community Dynamics ◽

Microbial Community Composition ◽

The Black Sea ◽

Ecological Niches ◽

Rrna Gene ◽

Similar Species ◽

Microbial Community Dynamics

Abstract The Black Sea is a unique environment having a thin layer of oxic-zone above and anoxic-zone below. Seasonal, vertical, and horizontal microbial assemblages were studied in terms of diversity, abundance, community structure using NGS of the 16S rRNA gene. Total of 750 bacteria species from 23 different phyla were identified. The number of species richness increased from the surface to deeper zones. Although microbial community compositions between sampling stations were similar, microbial community compositions were significantly different vertically between zones. Community compositions of the seawater and sediment were also significantly different. Community composition at 5 meters in summer was significantly different from other seasons, while remaining depths appeared similar. Species of nitrite-oxidizing, sulfate-reducing, thiosulfate reducing, Iron-reducing, Fe-Mn reducing and electricity-producing bacteria were reported for the first time in the Black Sea. Proteobacteria dominated all the sampling depths. Proteobacteria, Cyanobacteria, Bacteroidetes, and Verrucomicrobia were present in the whole water column, while Nitrospinae, Chloroflexi, and Kiritimatiellaeota were restricted, appearing abundant at 75 meters and deeper layers. Vertical microbial community composition variation is attributable to environmental factors and their adaptations to the various ecological niches.

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Benchmarking laboratory processes to characterise low-biomass respiratory microbiota

Scientific Reports ◽

10.1038/s41598-021-96556-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raiza Hasrat ◽

Jolanda Kool ◽

Wouter A. A. de Steenhuijsen Piters ◽

Mei Ling J. N. Chu ◽

Sjoerd Kuiling ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Positive Control ◽

Rrna Gene ◽

Elution Buffer ◽

Community Profile ◽

Microbial Community Profile ◽

Microbial Dna ◽

Pcr Conditions

AbstractThe low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.

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

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11475-9 ◽

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

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Alterations in microbial community composition with increasing <i>f</i>CO<sub>2</sub>: a mesocosm study in the eastern Baltic Sea

Biogeosciences ◽

10.5194/bg-14-3831-2017 ◽

2017 ◽

Vol 14 (16) ◽

pp. 3831-3849 ◽

Cited By ~ 10

Author(s):

Katharine J. Crawfurd ◽

Santiago Alvarez-Fernandez ◽

Kristina D. A. Mojica ◽

Ulf Riebesell ◽

Corina P. D. Brussaard

Keyword(s):

Microbial Community ◽

Ocean Acidification ◽

Baltic Sea ◽

Community Dynamics ◽

Inorganic Nitrogen ◽

Microbial Community Composition ◽

Cell Diameter ◽

Viral Lysis ◽

Nitrogen And Phosphorus ◽

Eastern Baltic

Abstract. Ocean acidification resulting from the uptake of anthropogenic carbon dioxide (CO2) by the ocean is considered a major threat to marine ecosystems. Here we examined the effects of ocean acidification on microbial community dynamics in the eastern Baltic Sea during the summer of 2012 when inorganic nitrogen and phosphorus were strongly depleted. Large-volume in situ mesocosms were employed to mimic present, future and far future CO2 scenarios. All six groups of phytoplankton enumerated by flow cytometry ( <  20 µm cell diameter) showed distinct trends in net growth and abundance with CO2 enrichment. The picoeukaryotic phytoplankton groups Pico-I and Pico-II displayed enhanced abundances, whilst Pico-III, Synechococcus and the nanoeukaryotic phytoplankton groups were negatively affected by elevated fugacity of CO2 (fCO2). Specifically, the numerically dominant eukaryote, Pico-I, demonstrated increases in gross growth rate with increasing fCO2 sufficient to double its abundance. The dynamics of the prokaryote community closely followed trends in total algal biomass despite differential effects of fCO2 on algal groups. Similarly, viral abundances corresponded to prokaryotic host population dynamics. Viral lysis and grazing were both important in controlling microbial abundances. Overall our results point to a shift, with increasing fCO2, towards a more regenerative system with production dominated by small picoeukaryotic phytoplankton.

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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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Microbial community dynamics of surface water in British Columbia, Canada

10.1101/719146 ◽

2019 ◽

Author(s):

Miguel I. Uyaguari-Diaz ◽

Matthew A. Croxen ◽

Kirby Cronin ◽

Zhiyao Luo ◽

Judith Isaac-Renton ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Fecal Contamination ◽

Rrna Gene ◽

Microbial Culture ◽

Sample Collection ◽

Fecal Indicator ◽

E Coli

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such as Escherichia coli, often tested as a weekly grab sample. To understand the stability of E.coli concentrations over time, we evaluated three approaches to measuring E. coli levels in water: microbial culture using Colilert, quantitative PCR for uidA and next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period. Enterobacteriaceae comprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities of E. coli compared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such as Prevotella and Bacteroides showed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.

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The Koala (Phascolarctos cinereus) faecal microbiome differs with diet in a wild population

PeerJ ◽

10.7717/peerj.6534 ◽

2019 ◽

Vol 7 ◽

pp. e6534 ◽

Cited By ~ 13

Author(s):

Kylie L. Brice ◽

Pankaj Trivedi ◽

Thomas C. Jeffries ◽

Michaela D.J. Blyton ◽

Christopher Mitchell ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Microbial Community Composition ◽

Plant Secondary Metabolites ◽

Free Access ◽

Rrna Gene ◽

Phascolarctos Cinereus ◽

Gut Microbes ◽

Principal Coordinates ◽

Unweighted Unifrac

BackgroundThe diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genusEucalyptus(family Myrtaceae).Eucalyptusproduces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet.MethodThe 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious speciesEucalyptus viminalis, the other comprising the less preferred and less digestible speciesEucalyptus obliqua.ResultsAlpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eatingE. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, theE. viminalisdiet produced communities dominated by the generaParabacteroidesand/orBacteroides, whereas theE. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae.DiscussionWe show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identifiedParabacteroidesand Ruminococcaceae genomes.

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