Capacity Of Microbial Communities Research Articles

In situ aerobic methane oxidation rates in a stratified lake

AbstractMicrobial aerobic methane oxidation is an important sink for aquatic methane worldwide. Despite its importance to global methane fluxes, few aerobic methane oxidation rates have been obtained in freshwater or marine environments without imposing changes to the microbial community through use of ex situ methods. A novel in situ incubation method for continuous time‐series measurements was used in Jordan Lake, North Carolina, during 2020–2021, to determine reaction kinetics for aerobic methane oxidation rates across a wide range of naturally varying methane (55–1833 nM) and dissolved oxygen (DO; 28–366 μM) concentrations and temperatures (17–30°C). Methane oxidation began immediately at the start of each of 21 incubations and methane oxidation rates were 1st order with respect to methane. The data density allowed for accurate calculation of 1st‐order rate constants, k, that ranged from 0.018 to 0.462 h−1 (R2 > 0.967). Addition of ammonium (20–45 μM) to natural concentrations ranging from 0.057 to 2.4 μM did not change aerobic methane oxidation rate kinetics, suggesting that the natural population of aerobic methane oxidizers in this eutrophic lake was not nitrogen limited. Values of k inversely correlated most strongly with initial DO concentrations (R2 = 0.82) rather than temperature. Values for k increased with Julian day throughout our sampling period, suggesting seasonal influences on methane oxidation via responses to geochemical changes or shifts in microbial community abundance and composition. These experiments demonstrate a high variability in the enzymatic capacity for 1st‐order methane oxidation rates in this eutrophic lake that is tightly and inversely coupled to oxygen concentrations. Measurements of in situ aerobic methane oxidation rate constants allow for the direct quantification and modeling of the microbial community's capacity for methane oxidation over a wide range of natural methane concentrations.

Combined effects of microplastics and cadmium on the soil-plant system: Phytotoxicity, Cd accumulation and microbial activity

Microplastics (MPs), an emerging pollutant of concern, widely cooccurred with heavy metals in soil, however, little is known about the combined effects of the interactions of MPs and cadmium (Cd) on the soil-plant system. In this study, the combined effects of several types of MPs and soil Cd contamination on Brassica juncea growth, Cd uptake, and soil microbial carbon metabolism were investigated in a 50-day pot experiment. Aged polyethylene (PE), aged polypropylene (PP), biodegradable polybutylene adipate terephthalate (PBAT) and polylactic acid (PLA) displayed moderate phytotoxicity, with reductions in leaf chlorophyll content and shoot biomass. Compared with the control treatment without MPs or B. juncea, B. juncea growth significantly increased the soil pH by 0.3 pH units, and the growth of B. juncea in the presence of biodegradable PBAT or PLA MPs increased the soil pH by an additional 0.4 or 0.6 pH units, respectively. The presence of PBAT or PLA MPs greatly reduced soil diethylenetriamine pentaacetic acid (DTPA)-extractable Cd concentrations and plant Cd accumulation. The Cd bioconcentration factor was higher in roots than shoots in all treatments except the treatment containing PBAT MPs. The average well color development (AWCD), an indicator of metabolic activity, was highest in the treatment with B. juncea alone and was reduced by both biodegradable and conventional MPs. The microbial utilization efficiency of esters and alcohols was enhanced in the treatment with PBAT MPs, whereas carboxylic acids were preferentially utilized in the treatment with PLA MPs. These findings indicate that co-exposure to MPs and Cd may alter soil microenvironmental characteristics such as soil pH, leading to changes in Cd bioavailability, plant growth and Cd accumulation, and the microbial community's capacity to metabolize carbon. These effects of MPs in soil warrant further exploration.

In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision

BackgroundHigh-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established.ResultsHere we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency.ConclusionOur benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.

Coupled Microbiological–Isotopic Approach for Studying Hydrodynamics in Deep Reservoirs: The Case of the Val d’Agri Oilfield (Southern Italy)

The studies upstream of the petroleum industry include oil and gas geological exploration and are usually focused on geological, structural, geophysical, and modeling techniques. In this research, the application of a coupled microbiological–isotopic approach was explored to assess its potential as an adequate characterization and monitoring tool of geofluids in oilfield areas, in order to expand and refine the information acquired through more consolidated practices. The test site was selected within the Val d’Agri oilfield, where some natural hydrocarbon springs have been documented since the 19th century in the Tramutola area. Close to these springs, several tens of exploration and production wells were drilled in the first half of the 20th century. The results demonstrated the effectiveness of the proposed approach for the analysis of fluid dynamics in complex systems, such as oilfield areas, and highlighted the capacity of microbial communities to “behave” as “bio-thermometers”, that is, as indicators of the different temperatures in various subsurface compartments.

Distributions and assemblages of microbial communities along a sediment core retrieved from a potential hydrate-bearing region offshore southwestern Taiwan

Assessing the impacts of methane released from hydrate-bearing environments on global carbon cycling would require detailed insights into the distributions and capacities of microbial communities at different horizons of sediment column. In this study, we conducted geochemical, gene abundance and diversity analyses for a sediment core retrieved from a potential hydrate-bearing region off southwestern Taiwan. Geochemical profiles were characterized by a sulfate-to-methane transition with decreasing total organic carbon and nitrogen in sediments, and increasing dissolved inorganic carbon, ammonium and total sulfur in sediments. Bacterial and archaeal 16S rRNA and amoA gene abundances decreased with depth. In contrast, ANME-1 and -2 16S rRNA gene abundances increased significantly across the sulfate-to-methane transition and peaked at different horizons below this interface. A total of 124,379 bacterial and 130,351 archaeal reads were recovered through tag-pyrosequencing of 16S rRNA genes and categorized into 9014 bacterial and 6394 archaeal operational taxonomic units on the basis of 97% sequence similarity, respectively. Major bacterial phyla/divisions and archaeal groups (>5% of the total reads) detected included Chloroflexi, Planctomycetes, OP9, Deltaproteobacteria, BHI80-139, MBG-B, Halobacteria, MCG, Thermoplasmata, ANME-1 and MG-I. The abundance variations of most major OTUs (>0.5% of the total reads) were statistically correlated with those of geochemical parameters. These lines of evidence suggest that the populations represented by the major OTUs or detected by group-specific primers were compartmentalized into different horizons and involved directly or indirectly in the cycling of methane, sulfate, organic carbon and nitrogen. Overall, this study demonstrates that the deep sequencing coverage combined with the quantification of gene abundance and geochemical characterization would enable to uncover the detailed distributions and potential metabolic capabilities of specific groups from complexly structured microbial communities in methane-rich marine sediments.

Direct comparison of individual substrate utilization from a CLPP study: A new analysis for metabolic diversity data

For over a decade, community level physiological profile (CLPP) assays, which assess a microbial community's capacity to metabolize specific sole carbon sources under defined laboratory conditions, have been popular for study of environmental soil samples. One such assay, BiOLOG™ allows for the colorimetric measurement of metabolism through the reduction of a tetrazolium dye, which yields optical density (OD) data for each substrate. Bacterial communities are extracted from soil and 150 μL of this extract is inoculated directly into each well of the microtitre plate. The combined metabolic data obtained are most often analyzed with multivariate statistical analyses, such as principal component analysis (PCA). The objectives of this study were (1) to develop a simple, visual, statistically valid method of determining community capabilities to utilize specific substrates in CLPP studies and (2) to test the number of samples needed for such discrimination to be reliable. This was done by direct comparison of the OD values obtained for two closely related microbial communities (surface and subsurface soil), plotted against a one-to-one ( y = x ) line. Due to variability in the portion of the soil microbial community inoculated into the individual test wells, the accuracy of the method was dependent on the number of replicates analyzed. A variety of data set sizes were tested, from n = 3 samples/soil depth to n = 40 samples/depth. The method was statistically valid for all data sets tested. Those substrates that deviated from the one-to-one line consistently had F values greater than 1. Additionally, data sets of n = 30 , 35 and 40 samples/depth consistently allowed identification of the eight substrates whose metabolism varied significantly between the two test soil communities. In conclusion, this one-to-one comparison has been shown to be a statistically valid analytical method to compare individual substrate usage between soils.

Competition of a parathion-hydrolyzing Flavobacterium with bacteria from ditch water in carbon-, nitrate- and phosphate-limited continuous cultures

Abstract The effect of competition for macroelements with bacteria from ditch water on the parathion-hydrolyzing Flavobacterium sp. ATCC 27551 (FB) was investigated within mixed continuous cultures under carbon-, nitrate- or phosphate-limited conditions. The high initial rate of parathion hydrolysis decreased rapidly in all cultures due to the loss of strain FB. Addition of 2-isopropyl-6-methyl-4-pyrimidinol (a selective source of carbon, nitrogen and energy for FB) to one nitrate- and carbon-limited chemostat caused a 20-fold increase in parathion-hydrolyzing activity compared to unamended control cultures and retention of FB. The presence of the parathion hydrolase-encoding gene could be demonstrated by a newly developed PCR detection method in all FB cultures during most of the cultivation period. These results suggest that competition effects cause the pesticide-degrading capacity of microbial communities depending on their frequency of exposure to the pesticide compounds.