scholarly journals Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation

2020 ◽  
Author(s):  
Elizabeth A. McDaniel ◽  
Benjamin Peterson ◽  
Sarah L.R. Stevens ◽  
Patricia Q. Tran ◽  
Karthik Anantharaman ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
Carbon Fixation ◽  
Inorganic Mercury ◽  
Metal Resistance ◽  
Anthropogenic Sources ◽  
Metabolic Flexibility ◽  
Mercury Methylation ◽  
Metabolic Diversity ◽  
Methylmercury Production

ABSTRACTMethylmercury is a potent, bioaccumulating neurotoxin that is produced by specific microorganisms by methylation of inorganic mercury released from anthropogenic sources. The hgcAB genes were recently discovered to be required for microbial methylmercury production in diverse anaerobic bacteria and archaea. However, the full phylogenetic and metabolic diversity of mercury methylating microorganisms has not been fully explored due to the limited number of cultured, experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury methylating microorganisms identified by hgcA sequence identity from publicly available isolate genomes and metagenome-assembled genomes (MAGs), as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known, and the distribution of hgcA is most likely due to several independent horizontal gene transfer events. Identified methylating microorganisms possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. Using a metatranscriptomic survey of a thawing permafrost gradient from which we identified 111 putative mercury methylators, we demonstrate that specific methylating populations may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify methylators based upon hgcA presence and describe their putative functions in the environment.IMPORTANCESpecific anaerobic microorganisms among the Deltaproteobacteria, Firmicutes, and Euryarchaeota have been shown to produce the bioaccumulating neurotoxin methylmercury. Accurately assessing the sources of microbial methylmercury production in the context of phylogenetic identification, metabolic guilds, and activity in the environment is crucial for understanding the constraints and effects of mercury impacted sites. Advances in next-generation sequencing technologies have enabled large-scale, cultivation-independent surveys of diverse and poorly characterized microorganisms of numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators, and their depth-discrete activities in the environment. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

scholarly journals Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Elizabeth A. McDaniel ◽  
Benjamin D. Peterson ◽  
Sarah L. R. Stevens ◽  
Patricia Q. Tran ◽  
Karthik Anantharaman ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
Carbon Fixation ◽  
Anaerobic Bacteria ◽  
Inorganic Mercury ◽  
Metal Resistance ◽  
Metabolic Flexibility ◽  
Metabolic Diversity ◽  
Content Type ◽  
Methylmercury Production

ABSTRACT Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment. IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

scholarly journals Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

2021 ◽  
Vol 97 (3) ◽  
Author(s):  
Constantinos Xenophontos ◽  
Martin Taubert ◽  
W Stanley Harpole ◽  
Kirsten Küsel
Keyword(s):  
Bacterial Communities ◽  
Species Interactions ◽  
Phylogenetic Diversity ◽  
Molecular Mechanisms ◽  
Linear Models ◽  
Theory Development ◽  
Metabolic Diversity ◽  
Community Functioning ◽  
Metabolic Functions ◽  
Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

scholarly journals Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

scholarly journals In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexusaggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

2021 ◽  
Vol 9 (3) ◽  
pp. 652
Author(s):  
Shigeru Kawai ◽  
Joval N. Martinez ◽  
Mads Lichtenberg ◽  
Erik Trampe ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Environmental Conditions ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Photosynthetic Bacterium ◽  
Early Morning ◽  
Metabolic Flexibility

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

Incorporating Concentration-Dependent Sediment Microbial Activity into Methylmercury Production Kinetics Modeling

2021 ◽  
Author(s):  
Grace E. Schwartz ◽  
Katherine A Muller ◽  
Saubhagya S Rathore ◽  
Regina L Wilpiszeski ◽  
Alyssa A Carrell ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Microbial Activity ◽  
Inorganic Mercury ◽  
Anaerobic Microorganisms ◽  
Kinetics Modeling ◽  
Production Kinetics ◽  
Anoxic Environments ◽  
Kinetics Of ◽  
Methylmercury Production

In anoxic environments, anaerobic microorganisms carrying the hgcAB gene cluster can mediate the transformation of inorganic mercury (Hg(II)) to monomethylmercury (MMHg). The kinetics of Hg(II) transformation to MMHg in periphyton...

scholarly journals Machine learning predicts large scale declines in native plant phylogenetic diversity

2020 ◽  
Vol 227 (5) ◽  
pp. 1544-1556 ◽  
Author(s):  
Daniel S. Park ◽  
Charles G. Willis ◽  
Zhenxiang Xi ◽  
John T. Kartesz ◽  
Charles C. Davis ◽  
...  
Keyword(s):  
Machine Learning ◽  
Phylogenetic Diversity ◽  
Large Scale ◽  
Native Plant

SECULAR VARIATIONS IN THE 14C CONCENTRATION OF DOUGLAS FIR TREE RINGS

1966 ◽  
Vol 3 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Willy Dyck
Keyword(s):  
Large Scale ◽  
Carbon Fixation ◽  
Douglas Fir ◽  
Sunspot Activity ◽  
Short Term ◽  
Fixation Rate ◽  
Pumping Rate ◽  
Counting Error ◽  
Annual Growth Rings

Measurements of the 14C concentration in a Douglas fir from Vancouver Island indicate a maximum variation of 44‰, during the past 1 100 years. The magnitude and trend of these variations are similar to those observed by de Vries (1958) in oak from Germany and by Willis et al. (1960) in sequoias from California, confirming earlier observations that atmospheric mixing of CO2 takes place rapidly on a large scale.14C measurements of successive annual growth rings from the piths of two firs (346 years and 1 142 years old) show no variations beyond those attributable to the statistical counting error of ± 6‰. Thus, cyclic variations in sunspot activity and (or) climate, if present during these intervals, did not affect the 14C concentration in the biosphere appreciably.A mechanism, based on a climate-sensitive carbon pumping rate of the biosphere coupled with the temperature-dependent oceanic CO2 content is postulated to explain, qualitatively, the observed short-term (150 years or less) and long-term (1 000 years or more) 14C variations in the land biosphere. Short-term fluctuations are directly proportional to temperature because variations in the carbon fixation rate lead to a pulsating CO2 content of the atmosphere. Long-term changes are inversely proportional to temperature because large quantities of carbon, normally stored in deeper regions of the ocean, are exchanged between biosphere and hydrosphere.

Study on Mercury Methylation in Sediment Using Enriched Stable Isotope Tracer

2011 ◽  
Vol 71-78 ◽  
pp. 3201-3206
Author(s):  
Yu Xiang Mao ◽  
Hai Lin Wang ◽  
Mei Wang
Keyword(s):  
Stable Isotope ◽  
Inorganic Mercury ◽  
Transformation Process ◽  
Florida Everglades ◽  
Mercury Methylation ◽  
Stable Isotope Tracer ◽  
Isotope Tracer ◽  
Incubation Experiments ◽  
Sediment Slurry ◽  
Risk Of Exposure

Methylmercury (MeHg) production from inorganic mercury in natural environment leads to bioaccumulation in fish, putting human being under the risk of exposure. This study investigated the transformation of enriched stable isotope tracer,199Hg2+, in sediment slurry of the Florida Everglades. Incubation experiments were conducted under four different laboratory conditions. The results suggest that methylation of mercury mainly happened under anaerobic condition, with microbial activity playing the major role. The relative methylation rate was determined to be 1% per day at the first few days, and then this transformation process slowed down. At the end of incubation experiment, totally around 20% of the isotope tracer199Hg2+was transformed to its methylated form, Me199Hg. This high potential of mercury methylation partially accounts for the contamination and bioaccumulation of MeHg in the relatively pristine Florida Everglades ecosystem.

scholarly journals A six year satellite-based assessment of the regional variations in aerosol indirect effects

2009 ◽  
Vol 9 (12) ◽  
pp. 4091-4114 ◽  
Author(s):  
T. A. Jones ◽  
S. A. Christopher ◽  
J. Quaas
Keyword(s):  
Large Scale ◽  
Vertical Motion ◽  
Aerosol Concentration ◽  
Anthropogenic Sources ◽  
Aerosol Layer ◽  
Relative Importance ◽  
Atmospheric Conditions ◽  
Anthropogenic Aerosol ◽  
Western Atlantic ◽  
Cloud Properties

Abstract. Aerosols act as cloud condensation nuclei (CCN) for cloud water droplets, and changes in aerosol concentrations have significant microphysical impacts on the corresponding cloud properties. Moderate Resolution Imaging Spectroradiometer (MODIS) aerosol and cloud properties are combined with NCEP Reanalysis data for six different regions around the globe between March 2000 and December 2005 to study the effects of different aerosol, cloud, and atmospheric conditions on the aerosol indirect effect (AIE). Emphasis is placed in examining the relative importance of aerosol concentration, type, and atmospheric conditions (mainly vertical motion) to AIE from region to region. Results show that in most regions, AIE has a distinct seasonal cycle, though the cycle varies in significance and period from region to region. In the Arabian Sea (AS), the six-year mean anthropogenic + dust AIE is −0.27 Wm−2 and is greatest during the summer months (<−2.0 Wm−2) during which aerosol concentrations (from both dust and anthropogenic sources) are greatest. Comparing AIE as a function of thin (LWP<20 gm−2) vs. thick (LWP≥20 gm−2) clouds under conditions of large scale ascent or decent at 850 hPa showed that AIE is greatest for thick clouds during periods of upward vertical motion. In the Bay of Bengal, AIE is negligible owing to less favorable atmospheric conditions, a lower concentration of aerosols, and a non-alignment of aerosol and cloud layers. In the eastern North Atlantic, AIE is weakly positive (+0.1 Wm−2) with dust aerosol concentration being much greater than the anthropogenic or sea salt components. However, elevated dust in this region exists above the maritime cloud layers and does not have a hygroscopic coating, which occurs in AS, preventing the dust from acting as CCN and limiting AIE. The Western Atlantic has a large anthropogenic aerosol concentration transported from the eastern United States producing a modest anthropogenic AIE (−0.46 Wm−2). Anthropogenic AIE is also present off the West African coast corresponding to aerosols produced from seasonal biomass burning (both natural and man-made). Interestingly, atmospheric conditions are not particularly favorable for cloud formation compared to the other regions during the times where AIE is observed; however, clouds are generally thin (LWP<20 gm−2) and concentrated very near the surface. Overall, we conclude that vertical motion, aerosol type, and aerosol layer heights do make a significant contribution to AIE and that these factors are often more important than total aerosol concentration alone and that the relative importance of each differs significantly from region to region.

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