scholarly journals Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

2020 ◽  
Author(s):  
Chelsea L. Murphy ◽  
Peter F. Dunfield ◽  
Andriy Sheremet ◽  
John R. Spear ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Global Analysis ◽  
Photosynthetic Reaction Center ◽  
Freshwater Ecosystems ◽  
Specific Substrate ◽  
Alkane Degradation ◽  
Microbial Genomes ◽  
Metabolic Versatility ◽  
Wide Range ◽  
Globally Distributed ◽  
Alkane Hydroxylases

AbstractThe recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β and γ carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatota’s preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.

scholarly journals Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

2020 ◽  
Author(s):  
Chelsea Murphy ◽  
Peter Dunfield ◽  
Andriy Sheremet ◽  
John Spear ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Global Analysis ◽  
Photosynthetic Reaction Center ◽  
Freshwater Ecosystems ◽  
Specific Substrate ◽  
Alkane Degradation ◽  
Microbial Genomes ◽  
Metabolic Versatility ◽  
Wide Range ◽  
Globally Distributed ◽  
Alkane Hydroxylases

Abstract The recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β and γ carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatota’s preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.

scholarly journals Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities

mBio ◽  
2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Chelsea L. Murphy ◽  
Andriy Sheremet ◽  
Peter F. Dunfield ◽  
John R. Spear ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Genomic Analysis ◽  
Freshwater Ecosystems ◽  
Marine Sponges ◽  
Comparative Genomic ◽  
Specific Substrate ◽  
Biosynthetic Pathways ◽  
Wide Range ◽  
Globally Distributed ◽  
Alkane Hydroxylases

ABSTRACT The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion. IMPORTANCE A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.

scholarly journals Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Sarahi L. Garcia ◽  
Maliheh Mehrshad ◽  
Moritz Buck ◽  
Jackson M. Tsuji ◽  
Josh D. Neufeld ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Carbon Sources ◽  
Natural Populations ◽  
Freshwater Ecosystems ◽  
Electron Donors ◽  
Functional Ecology ◽  
Lake Ecosystems ◽  
Tropical Regions ◽  
Metabolic Versatility ◽  
Globally Distributed

ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

scholarly journals Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations

2020 ◽  
Author(s):  
Sarahi L. Garcia ◽  
Maliheh Mehrshad ◽  
Moritz Buck ◽  
Jackson M. Tsuji ◽  
Josh D. Neufeld ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Carbon Sources ◽  
Natural Populations ◽  
Freshwater Ecosystems ◽  
Functional Ecology ◽  
Lake Ecosystems ◽  
Tropical Regions ◽  
Local Adaptations ◽  
Metabolic Versatility ◽  
Globally Distributed

AbstractPhotosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on their functional ecology and local adaptations came from isolates and merely 26 sequenced genomes that are poor representatives of natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-cell genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs) or “species”. Of the 71 mOTUs, 57 were classified as genus Chlorobium and these mOTUs varied in relative abundance up to ~60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many were lacking genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian Chlorobium clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insights into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.ImportanceThe reconstruction of genomes from metagenomes has enabled unprecedented insights into the ecology and evolution of environmental microbiomes. We applied this powerful approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and pinpoint nutrients that likely fuel their electron chains. Being photoautotrophs, these Chlorobia organisms also have the potential to serve as carbon sources that support metalimnetic and hypolimnetic food webs.

scholarly journals Global Analysis of Durable Policies for Free-Flowing River Protections

2021 ◽  
Vol 13 (4) ◽  
pp. 2347 ◽  
Author(s):  
Denielle Perry ◽  
Ian Harrison ◽  
Stephannie Fernandes ◽  
Sarah Burnham ◽  
Alana Nichols
Keyword(s):  
Global Analysis ◽  
Freshwater Ecosystems ◽  
Global Networks ◽  
Protection Mechanisms ◽  
The Creation ◽  
River Conservation ◽  
Protected Area Planning ◽  
Policy Types ◽  
Policy Mechanisms

Freshwater ecosystems are poorly represented in global networks of protected areas. This situation underscores an urgent need for the creation, application, and expansion of durable (long-term and enforceable) protection mechanisms for free-flowing rivers that go beyond conventional protected area planning. To address this need, we must first understand where and what types of protections exist that explicitly maintain the free-flowing integrity of rivers, as well as the efficacy of such policy types. Through policy analysis and an in-depth literature review, our study identifies three main policy mechanisms used for such protections: (1) River Conservation Systems; (2) Executive Decrees and Laws; and (3) Rights of Rivers. We found that globally only eight counties have national river conservation systems while seven countries have used executive decrees and similar policies to halt dam construction, and Rights of Rivers movements are quickly growing in importance, relative to other protection types. Despite the current extent of protection policies being insufficient to tackle the freshwater and biodiversity crises facing the world’s rivers, they do provide useful frameworks to guide the creation and expansion of protections. Ultimately, as countries act on global calls for protections, policy mechanisms must be tailored to their individual social and ecological geographies.

scholarly journals ASSESSMENT OF ECOLOGICAL STATE OF THE VELIKAYA RIVER DELTA BASED ON HYDROCHEMICAL INDICATORS AND STRUCTURE OF PHYTOPLANKTON

2017 ◽  
Vol 1 ◽  
pp. 82
Author(s):  
Tatiana Drozdenko ◽  
Sergei Mikhalap ◽  
Larisa Nikolskaya ◽  
Anna Chernova
Keyword(s):  
Water Quality ◽  
High Speed ◽  
Shannon Index ◽  
Freshwater Ecosystems ◽  
River Delta ◽  
Ecosystem Dynamics ◽  
Polluted Water ◽  
Ecological State ◽  
Sample Collection ◽  
Wide Range

The basis of the existence of freshwater ecosystems is phytoplankton, which produces most of the primary biological production, participates in repair processes and provides a wide range of ecosystem services. The short life cycle and high speed metabolism of microalgae make them ideal objects for ecological monitoring. The aim of the present study is to research the ecological state of the Velikaya river delta based on the species composition of phytoplankton community and some hydrochemical parameters. The sample collection for phytoplankton study and physicochemical measurements was carried out in summer 2016 at five stations representing different ecological locations of the Velikaya river delta. One hundred sixty five species taxa of microalgae belonging to 8 phylums were identified during the research: Bacillariophyta (37%), Chlorophyta (33.9%), Cyanophyta/Cyanobacteria (9.7%), Chrysophyta (6.1%), Euglenophyta (6.1%), Cryptophyta (3%), Dinophyta (3%), Xanthophyta (1.2%). The values of Shannon index indicate the average complexity of the microalgae communities structure. Values of Margalef index characterize the Velikaya river delta as an area of high species richness. Compared to the previous studies, a significant increase in the level of information diversity is observed, indicating an increase in the number of possible flows of substance and energy in the ecosystem. Dynamics of biogen substances in the water shows a slight increase of their concentrations. Ecological and geographical analysis proves that absolute dominance of cosmopolitan freshwater forms is typical for the algoflora of the Velikaya river delta. In relation to the pH-reaction inhabitants of neutral and slightly alkaline water dominate. Pantle–Buck saprobity index is applied for water quality assessment, which shows beta-mesosaprobic water quality in the ecosystem. Thus, the water of the Velikaya river delta could be referred to the category of moderately polluted water (class II of water quality). This is confirmed by the data of hydrochemical analysis.

scholarly journals DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data

2020 ◽  
Vol 1 (2) ◽  
pp. 209-224 ◽  
Author(s):  
Luis Fábregas Ibáñez ◽  
Gunnar Jeschke ◽  
Stefan Stoll
Keyword(s):  
Electron Paramagnetic Resonance ◽  
Software Package ◽  
Method Development ◽  
Electron Paramagnetic Resonance Spectroscopy ◽  
Global Analysis ◽  
Resonance Spectroscopy ◽  
Paramagnetic Resonance ◽  
Least Squares Fit ◽  
Wide Range ◽  
Electron Paramagnetic

Abstract. Dipolar electron paramagnetic resonance (EPR) spectroscopy (DEER and other techniques) enables the structural characterization of macromolecular and biological systems by measurement of distance distributions between unpaired electrons on a nanometer scale. The inference of these distributions from the measured signals is challenging due to the ill-posed nature of the inverse problem. Existing analysis tools are scattered over several applications with specialized graphical user interfaces. This renders comparison, reproducibility, and method development difficult. To remedy this situation, we present DeerLab, an open-source software package for analyzing dipolar EPR data that is modular and implements a wide range of methods. We show that DeerLab can perform one-step analysis based on separable non-linear least squares, fit dipolar multi-pathway models to multi-pulse DEER data, run global analysis with non-parametric distributions, and use a bootstrapping approach to fully quantify the uncertainty in the analysis.

scholarly journals Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

2016 ◽  
Vol 82 (9) ◽  
pp. 2854-2861 ◽  
Author(s):  
Omri M. Finkel ◽  
Tom O. Delmont ◽  
Anton F. Post ◽  
Shimshon Belkin
Keyword(s):  
High Salinity ◽  
Stress Factors ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Contig Assembly ◽  
Bacterial Populations ◽  
Content Type ◽  
Light Sensing ◽  
Wide Range ◽  
Globally Distributed

ABSTRACTThe leaves ofTamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10Tamarix aphyllatrees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, andFirmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting theTamarixphyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat.IMPORTANCEPlant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert treeTamarix aphylla. Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.

scholarly journals Hybridization between sympatric hammerhead sharks in the western North Atlantic Ocean

2019 ◽  
Vol 15 (4) ◽  
pp. 20190004 ◽  
Author(s):  
Amanda M. Barker ◽  
Douglas H. Adams ◽  
William B. Driggers ◽  
Bryan S. Frazier ◽  
David S. Portnoy
Keyword(s):  
Atlantic Ocean ◽  
First Generation ◽  
North Atlantic Ocean ◽  
Western Atlantic ◽  
Sphyrna Lewini ◽  
Scalloped Hammerhead ◽  
Wide Range ◽  
Hammerhead Sharks ◽  
Conservation Concern ◽  
Globally Distributed

Hybridization between closely related species has been documented across a wide range of taxa but has not been well studied in elasmobranchs. Hammerhead sharks have drawn global conservation concern because they experience some of the highest mortality rates among sharks when interacting with fisheries. Here we report on the detection of hybrids between the globally distributed scalloped hammerhead ( Sphyrna lewini ) and recently described Carolina hammerhead ( S. gilberti ) which are only known from the western Atlantic Ocean. Using a genomics approach, 10 first-generation hybrids and 15–17 backcrosses were detected from 554 individuals. The identification of backcrosses demonstrates hybrids are viable, and all backcrosses but one involved a scalloped hammerhead. All hybrids but one possessed Carolina hammerhead mtDNA, indicating sex-biased gene flow between species. Repeated hybridization and backcrossing with scalloped hammerheads could lead to the loss of endemic Carolina hammerheads.

What geckos are – an ecological-biogeographic perspective

2019 ◽  
Vol 66 (3-4) ◽  
pp. 253-263 ◽  
Author(s):  
Shai Meiri
Keyword(s):  
Survival Rates ◽  
Large Degree ◽  
Body Temperatures ◽  
Similar Activity ◽  
Wide Range ◽  
Low Latitudes ◽  
Preferred Temperatures ◽  
Biological Attributes ◽  
Globally Distributed ◽  
Activity Times

Geckos are a hyper-diverse, ancient, and globally distributed group. They have diverged early from other squamates and thus can be expected to differ from them along multiple ecological, life history, and biogeographic axes. I review a wide range of gecko traits, comparing them to those of other lizard taxa, to identify the unique, and unifying, attributes of geckos among lizards, based on comprehensive databases of lizard distributions and biological attributes. Few traits completely separate geckos from other lizard taxa, yet they differ to a large degree along many axes: they are more restricted to low latitudes and altitudes, are especially diverse on islands, but relatively scarce in America. They are small lizards, that lay small, fixed clutch sizes, for which they compensate only partially by laying frequently. Because they mature at relatively similar ages and have similar lifespans to other lizards, geckos produce fewer offspring over a year, and over their lifetimes, perhaps implying that they enjoy higher survival rates. While being the only large lizard clade of predominantly nocturnal lizards a large proportion of species is active by day. Gecko body temperatures and preferred temperatures are lower than those of other lizards –even when they are compared to lizards with similar activity times. Worryingly, most geckos have small ranges that often reside completely outside of protected areas – much more frequently than in other reptile and vertebrate taxa.

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