scholarly journals Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins

2021 ◽  
Author(s):  
P. Maza-Márquez ◽  
M. D. Lee ◽  
A. M. Detweiler ◽  
B. M. Bebout
Keyword(s):  
Nitrogen Cycling ◽  
Nitrogen Metabolism ◽  
Microbial Mats ◽  
Ammonia Oxidizing Bacteria ◽  
Free Oxygen ◽  
Metagenome Analysis ◽  
Oxygen Gradient ◽  
The Earth ◽  
Genes Encoding ◽  
Metagenome Sequencing

AbstractMicrobial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. BLAST analysis of some transcribed proteins indicated that they likely functioned as a nitrate reductase. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.

scholarly journals Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 389
Author(s):  
Pia Marter ◽  
Sixing Huang ◽  
Henner Brinkmann ◽  
Silke Pradella ◽  
Michael Jarek ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Morphological Diversity ◽  
Cell Types ◽  
Phylogenetic Position ◽  
Metagenome Analysis ◽  
New Family ◽  
Metagenome Sequencing ◽  
Axenic Strains ◽  
Reliable Classification ◽  
Metagenomic Assembly

Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.

scholarly journals Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. e01966-18 ◽  
Author(s):  
Genis Andrés Castillo Villamizar ◽  
Heiko Nacke ◽  
Marc Boehning ◽  
Kristin Herz ◽  
Rolf Daniel
Keyword(s):  
Phosphatase Activity ◽  
High Performance ◽  
Cell Metabolism ◽  
Screening Method ◽  
Phosphorus Cycle ◽  
Functional Metagenomics ◽  
Phosphorus Pollution ◽  
Metagenome Analysis ◽  
Genes Encoding ◽  
Novel Target

ABSTRACTPhosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments.IMPORTANCEPhosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth’s phosphatase pools.

Genetic regulation of nitrogen metabolism in the fungi

1997 ◽  
Vol 61 (1) ◽  
pp. 17-32
Author(s):  
G A Marzluf
Keyword(s):  
Nitrogen Metabolism ◽  
Protein Interactions ◽  
Fungal Pathogens ◽  
Metabolic Regulation ◽  
Specific Binding ◽  
Genetic Regulation ◽  
Nitrogen Sources ◽  
Specific Protein ◽  
Genes Encoding ◽  
Gata Family

In the fungi, nitrogen metabolism is controlled by a complex genetic regulatory circuit which ensures the preferential use of primary nitrogen sources and also confers the ability to use many different secondary nitrogen sources when appropriate. Most structural genes encoding nitrogen catabolic enzymes are subject to nitrogen catabolite repression, mediated by positive-acting transcription factors of the GATA family of proteins. However, certain GATA family members, such as the yeast DAL80 factor, act negatively to repress gene expression. Selective expression of the genes which encode enzymes for the metabolism of secondary nitrogen sources is often achieved by induction, mediated by pathway-specific factors, many of which have a GAL4-like C6/Zn2 DNA binding domain. Regulation within the nitrogen circuit also involves specific protein-protein interactions, as exemplified by the specific binding of the negative-acting NMR protein with the positive-acting NIT2 protein of Neurospora crassa. Nitrogen metabolic regulation appears to play a significant role in the pathogenicity of certain animal and plant fungal pathogens.

scholarly journals Changes of Soil Microbes Related with Carbon and Nitrogen Cycling after Long-Term CO2 Enrichment in a Typical Chinese Maize Field

2020 ◽  
Vol 12 (3) ◽  
pp. 1250 ◽  
Author(s):  
Tiantian Diao ◽  
Zhengping Peng ◽  
Xiaoguang Niu ◽  
Rongquan Yang ◽  
Fen Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
Nitrogen Cycling ◽  
Relative Abundance ◽  
Soil Microbes ◽  
Inorganic Nitrogen ◽  
Ammonia Oxidizing Bacteria ◽  
Rhizospheric Soil ◽  
Carbon And Nitrogen ◽  
Carbon And Nitrogen Cycling ◽  
Maize Field

Elevated atmospheric CO2 concentration (eCO2) has been the most important driving factor and characteristic of climate change. To clarify the effects of eCO2 on the soil microbes and on the concurrent status of soil carbon and nitrogen, an experiment was conducted in a typical summer maize field based on a 10-year mini FACE (Free Air Carbon Dioxide Enrichment) system in North China. Both rhizospheric and bulk soils were collected for measurement. The soil microbial carbon (MBC), nitrogen (MBN), and soil mineral N were measured at two stages. Characteristics of microbes were assayed for both rhizospheric soil and bulk soils at the key stage. We examined the plasmid copy numbers, diversities, and community structures of bacteria (in terms of 16s rRNA), fungi (in terms of ITS-internal transcribed spacer), ammonia oxidizing bacteria (AOB) and denitrifiers including nirK, nirS, and nosZ using the Miseq sequencing technique. Results showed that under eCO2 conditions, both MBC and MBN in rhizospheric soil were increased significantly. The quantity of ITS was increased in the eCO2 treatment compared with that in the ambient CO2 (aCO2) treatment, while the quantity of 16s rRNA in rhizospheric soil showed decrease in the rhizospheric soil in the eCO2 treatment. ECO2 changed the relative abundance of microbes in terms of compositional proportion of some orders or genera particularly in the rhizospheric soil-n particular, Chaetomium increased for ITS, Subgroups 4 and 6 increased for 16s rRNA, Nitrosospira decreased for AOB, and some genera showed increase for nirS, nirK, and nosZ. Nitrate N was the main inorganic nitrogen form at the tasseling stage and both quantities of AOB and denitrifiers, as well as the nosZ/(nirS+nirK) showed an increase under eCO2 conditions particularly in the rhizospheric soil. The Nitrosospira decreased in abundance under eCO2 conditions in the rhizospheric soil and some genera of denitrifiers also showed differences in abundance. ECO2 did not change the diversities of microbes significantly. In general, results suggested that 10 years of eCO2 did affect the active component of C and N pools (such as MBC and MBN) and both the quantities and relative abundance of microbes which are involved in carbon and nitrogen cycling, possibly due to the differences in both the quantities and component of substrate for relevant microbes in the rhizospheric soils.

scholarly journals Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge

2019 ◽  
Vol 7 (12) ◽  
pp. 713 ◽  
Author(s):  
Chenbing Ai ◽  
Zhang Yan ◽  
Han Zhou ◽  
Shanshan Hou ◽  
Liyuan Chai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Glutamine Synthetase ◽  
Activated Sludge ◽  
Temperature Variation ◽  
Nitrogen Metabolism ◽  
Metagenomic Data ◽  
Seasonal Temperature ◽  
Simulated Temperature ◽  
Genes Encoding ◽  
Seasonal Temperature Variation

It is well acknowledged that the activities of activated sludge (AS) are influenced by seasonal temperature variation. However, the underlying mechanisms remain largely unknown. Here, the activities of activated sludge under three simulated temperature variation trends were compared in lab-scale. The TN, HN3-H, and COD removal activities of activated sludge were improved as temperature elevated from 20 °C to 35 °C. While, the TN, HN3-H, COD and total phosphorus removal activities of activated sludge were inhibited as temperature declined from 20 °C to 5 °C. Both the extracellular polymer substances (EPS) composition (e.g., total amount, PS, PN and DNA) and sludge index of activated sludge were altered by simulated seasonal temperature variation. The variation of microbial community structures and the functional potentials of activated sludge were further explored by metagenomics. Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla for each activated sludge sample under different temperatures. However, the predominant genera of activated sludge were significantly modulated by simulated temperature variation. The functional genes encoding enzymes for nitrogen metabolism in microorganisms were analyzed. The enzyme genes related to ammonification had the highest abundance despite the changing temperature, especially for gene encoding glutamine synthetase. With the temperature raising from 20 °C to 35 °C. The abundance of amoCAB genes encoding ammonia monooxygenase (EC:1.14.99.39) increased by 305.8%. Meanwhile, all the enzyme genes associate with denitrification were reduced. As the temperature declined from 20 °C to 5 °C, the abundance of enzyme genes related to nitrogen metabolism were raised except for carbamate kinase (EC:2.7.2.2), glutamate dehydrogenase (EC:1.4.1.3), glutamine synthetase (EC:6.3.1.2). Metagenomic data indicate that succession of the dominant genera in microbial community structure is, to some extent, beneficial to maintain the functional stability of activated sludge under the temperature variation within a certain temperature range. This study provides novel insights into the effects of seasonal temperature variation on the activities of activated sludge.

scholarly journals Changes in the nitrogen biogeochemical cycle in sediments of an urban river under different dissolved oxygen levels

2018 ◽  
Vol 19 (4) ◽  
pp. 1271-1278 ◽  
Author(s):  
Yaping Zhang ◽  
Xiaohong Ruan ◽  
Wenli Shi
Keyword(s):  
Dissolved Oxygen ◽  
Nitrogen Cycling ◽  
Quantitative Polymerase Chain Reaction ◽  
Nitrogen Transformation ◽  
Urban River ◽  
Ammonia Oxidizing Bacteria ◽  
Urban Rivers ◽  
Ammonium Oxidation ◽  
Microbial Nitrogen ◽  
Concentration Changes

Abstract Urban rivers are considered as a hot spot of microbial nitrogen cycling due to extensive N loading. However, microbial nitrogen transformation dynamics in urban rivers with different dissolved oxygen (DO) conditions are still unclear. This study investigated the effects of DO concentration changes (anaerobic to aerobic) in overlying water on nitrogen-cycling gene abundance in incubation conditions using sediment from a typical urban river in the Yangtze River Delta. Quantitative polymerase chain reaction (qPCR) results revealed that the abundances of the nitrification gene amoA, denitrification gene nirS/K, norB, nosZ, and anammox gene hzo increased by one to two orders of magnitude from anaerobic to aerobic conditions. Ammonia-oxidizing archaea (AOA) predominated the ammonium oxidation microbial populations, about tenfold more than the ammonia-oxidizing bacteria (AOB) populations. Significant correlations were found among the abundances of AOA-amoA, AOB-amoA, nirS, nirK, and hzo genes, implying a close coupling of aerobic ammonium oxidation (AAO), denitrification, and anammox processes at the molecular level. Moreover, the nitrogen transformation rates were calculated using a box model linking the measured dissolved inorganic nitrogen species. The contribution of anammox to N2 production was 85% under saturated treatment, and the AAO rate was significantly positive correlated to the anammox rate. Our results suggested that coupled AAO and anammox might be the dominant pathway for reactive nitrogen removal in urban rivers with elevated DO levels.

scholarly journals Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

2010 ◽  
Vol 192 (12) ◽  
pp. 3033-3042 ◽  
Author(s):  
Marcel T. J. van der Meer ◽  
Christian G. Klatt ◽  
Jason Wood ◽  
Donald A. Bryant ◽  
Mary M. Bateson ◽  
...  
Keyword(s):  
National Park ◽  
Microbial Mats ◽  
Hot Spring ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Anoxygenic Phototrophs ◽  
Lipid Biomarker ◽  
Genes Encoding

ABSTRACT Roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in Yellowstone National Park. These strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rRNA, lipid distributions, and genomic and metagenomic sequences. Like a Japanese isolate, R. castenholzii, the Yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photoheterotrophically or chemoheterotrophically under dark aerobic conditions. The genome of one isolate, Roseiflexus sp. strain RS1, contains genes necessary to support these metabolisms. This genome also contains genes encoding the 3-hydroxypropionate pathway for CO2 fixation and a hydrogenase, which might enable photoautotrophic metabolism, even though neither isolate could be grown photoautotrophically with H2 or H2S as a possible electron donor. The isolates exhibit temperature, pH, and sulfide preferences typical of their habitat. Lipids produced by these isolates matched much better with mat lipids than do lipids produced by R. castenholzii or Chloroflexus isolates.

scholarly journals Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Lokeshwaran Manoharan ◽  
Jessica A. Kozlowski ◽  
Robert W. Murdoch ◽  
Frank E. Löffler ◽  
Filipa L. Sousa ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Life Forms ◽  
Central Carbon Metabolism ◽  
Rrna Gene ◽  
Environmental Distribution ◽  
Reductive Dehalogenase ◽  
Signature Genes ◽  
Genes Encoding ◽  
Eukaryote Evolution ◽  
Metagenome Sequencing

ABSTRACT The genomes of Asgard Archaea, a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota, we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki- and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry. IMPORTANCE Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them.

scholarly journals A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Junhua Li ◽  
Huanzi Zhong ◽  
Yuliaxis Ramayo-Caldas ◽  
Nicolas Terrapon ◽  
Vincent Lombard ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Production Systems ◽  
Wall Material ◽  
Rumen Microbes ◽  
Bovine Rumen ◽  
Degrading Enzymes ◽  
Genes Encoding ◽  
Health And Disease ◽  
Metagenome Sequencing ◽  
Available Information

Abstract Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

Sign in / Sign up

Export Citation Format

Share Document