1
|
Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments. Microbiol Spectr 2022; 10:e0035222. [PMID: 35647693 PMCID: PMC9241837 DOI: 10.1128/spectrum.00352-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs. IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.
Collapse
|
2
|
Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. FRONTIERS IN PLANT SCIENCE 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
Collapse
Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
| |
Collapse
|
3
|
Liu D, He X, Chater CCC, Perez-Moreno J, Yu F. Microbiome Community Structure and Functional Gene Partitioning in Different Micro-Niches Within a Sporocarp-Forming Fungus. Front Microbiol 2021; 12:629352. [PMID: 33859628 PMCID: PMC8042227 DOI: 10.3389/fmicb.2021.629352] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/10/2021] [Indexed: 02/03/2023] Open
Abstract
Thelephora ganbajun is a wild edible mushroom highly appreciated throughout China. The microbiomes of some fungal sporocarps have been studied, however, their potential functional roles currently remain uncharacterized. Here, functional gene microarrays (GeoChip 5.0) and amplicon sequencing were employed to define the taxonomic and functional attributes within three micro-niches of T. ganbajun. The diversity and composition of bacterial taxa and their functional genes differed significantly (p < 0.01) among the compartments. Among 31,117 functional genes detected, some were exclusively recorded in one sporocarp compartment: 1,334 genes involved in carbon (mdh) and nitrogen fixation (nifH) in the context; 524 genes influencing carbon (apu) and sulfite reduction (dsrB, dsra) in the hymenophore; and 255 genes involved in sulfur oxidation (soxB and soxC) and polyphosphate degradation (ppx) in the pileipellis. These results shed light on a previously unknown microbiome and functional gene partitioning in sporome compartments of Basidiomycota. This also has great implications for their potential ecological and biogeochemical functions, demonstrating a higher genomic complexity than previously thought.
Collapse
Affiliation(s)
- Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xinhua He
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, United States
| | - Caspar C. C. Chater
- Department of Natural Capital and Plant Health, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
4
|
Chukwuemeka PO, Umar HI, Olukunle OF, Oretade OM, Olowosoke CB, Akinsola EO, Elabiyi MO, Kurmi UG, Eigbe JO, Oyelere BR, Isunu LE, Oretade OJ. In silico design and validation of a highly degenerate primer pair: a systematic approach. J Genet Eng Biotechnol 2020; 18:72. [PMID: 33205353 PMCID: PMC7671957 DOI: 10.1186/s43141-020-00086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/21/2020] [Indexed: 11/18/2022]
Abstract
Background The techniques of amplifying genetic materials have enabled the extensive study of several biological activities outside the biological milieu of living systems. More recently, this approach has been extended to amplify population of genes, from evolutionarily related gene family for detection and evaluation of microbial consortial with several unique potentialities (e.g., enzymatic degradability). Conceivably, primer mixtures containing substitutions of different bases at specific sites (degenerate primers) have enabled the amplification of these genes in PCR reaction. However, the degenerate primer design problem (DPD) is a constraint to designing this kind of primer. To date, different algorithms now exist to solve various versions of DPD problem, many of which, only few addresses and satisfy the criteria to design primers that can extensively cover high through-put sequences while striking the balance between specificity and efficiency. The highly degenerate primer (HYDEN) design software program primarily addresses this variant of DPD problem termed “maximum coverage-degenerate primer design (MC-DPD)” and its heuristics have been substantiated for optimal efficiency from significant successes in PCR. In spite of the premium presented for designing degenerate primers, literature search has indicated relatively little use of its heuristics. This has been thought to result from the complexity of the program since it is run only by command-line, hence limiting its accessibility. To solve this problem, researchers have optionally considered the manual design of degenerate primers or design through software programs that provides accessibility through a graphical user interface (GUI). Realizing this, we have attempted in this study to provide a user-friendly approach for researchers with little or no background in bioinformatics to design degenerate primers using HYDEN Results Virtual Tests of our designed degenerate primer pair through in silico PCR substantiated the correspondence between efficiency and coverage with the target sequences as pre-defined by the initial HYDEN output, thereby validating the potentials of HYDEN to effectively solve the MC-DPD problem. Additionally, the designed primer-pair mechanistically amplified all sequences used as a positive control with no amplification observed in the negative controls. Conclusion In this study, we provided a turnkey protocol to simplify the design of degenerate primers using the heuristics of the HYDEN software program.
Collapse
|
5
|
Zaghmouri I, Michotey VD, Armougom F, Guasco S, Bonin PC. Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community. MARINE POLLUTION BULLETIN 2018; 130:76-83. [PMID: 29866572 DOI: 10.1016/j.marpolbul.2018.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera.
Collapse
Affiliation(s)
- Imen Zaghmouri
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Valerie D Michotey
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France.
| | - Fabrice Armougom
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Sophie Guasco
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Patricia C Bonin
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| |
Collapse
|
6
|
Guilger M, Pasquoto-Stigliani T, Bilesky-Jose N, Grillo R, Abhilash PC, Fraceto LF, Lima RD. Biogenic silver nanoparticles based on trichoderma harzianum: synthesis, characterization, toxicity evaluation and biological activity. Sci Rep 2017; 7:44421. [PMID: 28300141 PMCID: PMC5353535 DOI: 10.1038/srep44421] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/07/2017] [Indexed: 01/03/2023] Open
Abstract
White mold is an agricultural disease caused by the fungus Sclerotinia sclerotiorum, which affects important crops. There are different ways of controlling this organism, but none provides inhibition of its resistance structures (sclerotia). Nanotechnology offers promising applications in agricultural area. Here, silver nanoparticles were biogenically synthesized using the fungus Trichoderma harzianum and characterized. Cytotoxicity and genotoxicity were evaluated, and the nanoparticles were initially tested against white mold sclerotia. Their effects on soybean were also investigated with no effects observed. The nanoparticles showed potential against S. sclerotiorum, inhibiting sclerotia germination and mycelial growth. Nanoparticle characterization data indicated spherical morphology, satisfactory polydispersity and size distribution. Cytotoxicity and genotoxicity assays showed that the nanoparticles caused both the effects, although, the most toxic concentrations were above those applied for white mold control. Given the potential of the nanoparticles against S. sclerotiorum, we conclude that this study presents a first step for a new alternative in white mold control.
Collapse
Affiliation(s)
- Mariana Guilger
- Federal University of São Carlos, Sorocaba campus, Rodovia João Leme dos Santos, km 110, 18052-780, Sorocaba, Brazil
- Laboratory of Biotechnology, University of Sorocaba, Rodovia Raposo Tavares, km 92, 18023-000, Sorocaba, São Paulo, Brazil
| | - Tatiane Pasquoto-Stigliani
- Federal University of São Carlos, Sorocaba campus, Rodovia João Leme dos Santos, km 110, 18052-780, Sorocaba, Brazil
- Laboratory of Biotechnology, University of Sorocaba, Rodovia Raposo Tavares, km 92, 18023-000, Sorocaba, São Paulo, Brazil
| | - Natália Bilesky-Jose
- Laboratory of Biotechnology, University of Sorocaba, Rodovia Raposo Tavares, km 92, 18023-000, Sorocaba, São Paulo, Brazil
| | - Renato Grillo
- Center of Natural and Human Sciences, Federal University of ABC, Santo André, Brazil
| | - P. C. Abhilash
- Institute of Environment & Sustainable Development, Banaras Hindu University, Varanasi 221005, India
| | - Leonardo Fernandes Fraceto
- Laboratory of Environmental Nanotechnology, Department of Environmental Engineering, São Paulo State University (UNESP), Sorocaba, São Paulo, Brazil
| | - Renata de Lima
- Federal University of São Carlos, Sorocaba campus, Rodovia João Leme dos Santos, km 110, 18052-780, Sorocaba, Brazil
- Laboratory of Biotechnology, University of Sorocaba, Rodovia Raposo Tavares, km 92, 18023-000, Sorocaba, São Paulo, Brazil
| |
Collapse
|
7
|
Decleyre H, Heylen K, Van Colen C, Willems A. Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers. Front Microbiol 2015; 6:1124. [PMID: 26528270 PMCID: PMC4604302 DOI: 10.3389/fmicb.2015.01124] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6 m), with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celeribacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms.
Collapse
Affiliation(s)
- Helen Decleyre
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Carl Van Colen
- Marine Biology Research Group, Department of Biology, Ghent University Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| |
Collapse
|
8
|
Laverock B, Tait K, Gilbert JA, Osborn AM, Widdicombe S. Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:113-21. [PMID: 24596269 PMCID: PMC4208606 DOI: 10.1111/1758-2229.12115] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/11/2013] [Indexed: 05/13/2023]
Abstract
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.
Collapse
Affiliation(s)
- B Laverock
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
- Department of Animal and Plant Sciences, University of SheffieldSheffield, S10 2TN, UK
- School of Plant Biology and the UWA Oceans Institute, University of Western AustraliaCrawley, WA, 6009, Australia
| | - K Tait
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
| | - J A Gilbert
- Argonne National Laboratory, Institute of Genomic and Systems Biology9700 South Cass Avenue, Argonne, IL, 60439, USA
- Department of Ecology and Evolution, University of Chicago5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - A M Osborn
- Department of Animal and Plant Sciences, University of SheffieldSheffield, S10 2TN, UK
- Department of Biological Sciences, University of HullHull, HU6 7RX, UK
- School of Life Sciences, University of Lincoln, Brayford PoolLincoln, LN6 7TS, UK
| | - S Widdicombe
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
| |
Collapse
|
9
|
Rusch A, Gaidos E. Nitrogen-cycling bacteria and archaea in the carbonate sediment of a coral reef. GEOBIOLOGY 2013; 11:472-484. [PMID: 23849004 DOI: 10.1111/gbi.12048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 06/10/2013] [Indexed: 06/02/2023]
Abstract
In the coarse-grained carbonate sediments of coral reefs, advective porewater flow and the respiration of organic matter establish redox zones that are the scene of microbially mediated transformations of N compounds. To investigate the geobiology of N cycling in reef sediments, the benthic microbiota of Checker Reef in Kaneohe Bay, Hawaii, were surveyed for candidate nitrate reducers, ammonifying nitrite reducers, aerobic and anaerobic ammonia oxidizers (anammox) by identifying phylotypes of their key metabolic genes (napA, narG, nrfA, amoA) and ribotypes (unique RNA sequences) of anammox-like 16S rRNA. Putative proteobacteria with the catalytic potential for nitrate reduction were identified in oxic, interfacial and anoxic habitats. The estimated richness of napA (≥202 in anoxic sediment) and narG (≥373 and ≥441 in oxic and interfacial sediment, respectively) indicates a diverse guild of nitrate reducers. The guild of nrfA hosts in interfacial reef sediment was dominated by Vibrio species. The identified members of the aerobic ammonium oxidizing guild (amoA hosts) were Crenarchaeota or close relatives of Nitrosomonadales. Putative anammox bacteria were detected in the RNA pool of Checker Reef sediment. More than half of these ribotypes show ≥90% identity with homologous sequences of Scalindua spp., while no evidence was found for members of the genera Brocadia or Kuenenia. In addition to exploring the diversity of these four nitrogen-cycling microbial guilds in coral reef sediments, the abundances of aerobic ammonium oxidizers (amoA), nitrite oxidizers (nxrAB), ammonifying nitrite reducers (nrfA) and denitrifiers (nosZ) were estimated using real-time PCR. Representatives of all targeted guilds were detected, suggesting that most processes of the biogeochemical N cycle can be catalyzed by the benthic microbiota of tropical coral reefs.
Collapse
Affiliation(s)
- A Rusch
- Department of Geology and Geophysics, University of Hawaii at Mānoa, Honolulu, HI, USA.
| | | |
Collapse
|