New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment
Abstract
:1. Introduction
2. The Start: 16S rRNA Genes for Studies in the Environment
3. Progress and Limitations of Sequence Studies of 16S rRNA Genes and Metagenomes
4. Functional Gene Studies
5. Photosynthesis and Anoxygenic Phototrophic Bacteria
5.1. The Phylogeny of the fmoA Gene in Green Sulfur Bacteria
5.2. The Phylogeny of the pufLM Genes in Purple Sulfur Bacteria
5.3. Molecular Ecology and Species Recognition of Phototrophic Sulfur Bacteria in the Environment
5.4. Environmental Communities of Green Sulfur Bacteria
5.5. Environmental Communities of Phototrophic Purple Bacteria
5.6. Baltic Sea Coastal Lagoon
5.7. Salt Lakes of the Salar de Atacama
5.8. Biodiversity of the bchY Gene
6. Oxidation and Reduction of Sulfur Compounds
6.1. Adenosine-5′-Phosphosulfate Reductase (APS Reductase), aprA
6.2. Dissimilatory Sulfite Reductase, dsrAB
6.3. Sulfate Thioesterase, soxB
7. Denitrification
7.1. Dissimilatory Nitrate Reductases, narH, narG and napA
7.2. Dissimilatory Nitrite Reductases, nirS and nirK
8. Nitrification—Oxidation of Ammonia—amoA
8.1. Aerobic Ammonia-Oxidizing Bacteria (AOB)
8.2. Ammonia-Oxidizing Archaea (AOA)
8.3. Anaerobic Ammonia-Oxidizing Bacteria (Anammox)
9. Oxidation of Methane—Methane Monooxygenase pmoA
10. Biosynthetic Pathways of Deep Sea Hot Vent Microorganisms
10.1. The Logatchev Hydrothermal Vent Field
10.2. Lamellibrachia Anaximandri
10.3. Rimicaris Exoculata
11. Conclusions
11.1. Functional Diversity—The Competition of Pathways in Nature
11.2. Environmental Conditions Determine Microbial Community Structure
11.3. The Challenges of Functional Diversity Studies in the Habitat
11.4. Selective Enrichment of Functional Groups
Acknowledgments
References
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Gene | Biogeochemical Fucnction | Gene Product | Primer Name | Primer Sequence (5'-3') | Reference |
---|---|---|---|---|---|
pufLM | photosynthesis | photosynthetic reaction center | pufL67F | TTCGACTTYTGGRTNGGNCC | [48] |
pufM781R | CCAKSGTCCAGCGCCAGAANA | [48] | |||
fmoA | photosynthesis | bacteriochlorophyll-a-protein | F-Start-fmo-modif | ATT ATG GCT CTN TTC GGC | [75] |
r-889-FMO | CCGACCATNCCGTGRTG | [47] | |||
bchlY | photosynthesis | chlorophyllide reductase | bchY-fwd | CCNCARACNATGTGYCCNGCNTTYGG | [19] |
bchY-rev | GGRTCNRCNGGRAANATYTCNCCC | [19] | |||
soxB | “sulfur” oxidation | sulfate thioesterase | soxB432F | GAYGGNGGNGAYACNTGG | [96] |
soxB1446B | CATGTCNCCNCCRTGYTG | [96] | |||
aprA | “sulfur” oxidation | APS reductase | AprA-1-FW | TGGCAGATCATGATYMATGG | [20] |
sulfur reduction | AprA-5-rv | GCGCCAACYGGRCCTTA | [20] | ||
dsrAB | “sulfur” oxidation | dissimilatory disulfite reductase | rDSR1Fa | AARGGNTAYTGGAARG | [22] |
sulfur reduction | rDSR1Fb | TTYGGNTAYTGGAARG | [22] | ||
rDSR1Fc | ATGGGNTAYTGGAARG | [22] | |||
rDSR4Ra | CCRAARCAIGCNCCRCA | [22] | |||
rDSR4Rb | GGRWARCAIGCNCCRCA | [22] | |||
narH | nitrate reduction | dissimilatory nitrate reductase | narH50F | AARTGYATCGGYTGCCA | [8] |
denitrification | narH1040B | GTNCGRTYTCNGG | [8] | ||
narH403F | GGNCCNAACTGGGNGA | [8] | |||
narH403B | TCNTCCCAGTTNGGNCC | [8] | |||
nirS | nitrate reduction | dissimilatory nitrate reductase | nirS1F | CCTAYTGGCCGCCRCART | [123] |
denitrification | nirS6R | CGTTGAACTTRCCGGT | [123] | ||
nirK | nitrate reduction | dissimilatory nitrate reductase | nirK1F | GGMATGGTKCCSTGGCA | [123] |
denitrification | nirK5R | GCCTCGATCAGRTTRTGG | [123] | ||
Cunir3 | CGTCTAYCAYTCCGCVCC | [128] | |||
Cunir4 | GCCTCGATCAGRTTRTGG | [128] | |||
amoA | ammonia oxidation | ammonia monooxygenase | amoA-1F | GGGGTTTCTACTGGTGGT | [129] |
amoA-2R | CCCCTCKGSAAAGCCTTCTTC | [129] | |||
amoCAB | ammonia oxidation | ammonia monooxygenase | amoC58f | CTAYGACATGTCRCTGTGG | [130] |
amoB1179r | CCAAARCGRCTTTCCGG | [130] | |||
amoA | ammonia oxidation | archaeal | Arch-amoAF | STAATGGTCTGGCTTAGACG | [131] |
ammonia monooxygenase | Arch-amoAR | GCGGCCATCCATCTGTATGT | [131] | ||
anirKa | archaeal | anirKa-58F | ACBYTATTCGGAAGYACATACACA | [132] | |
dissimilatory nitrate reductase | anirKa-579R | GYMATTCCGTACATKCCGGA | [132] | ||
anirKb | archaeal | anirKb-61F | CTATTCGGARGTWCTTTYACTGC | [132] | |
dissimilatory nitrate reductase | anirKa-555R | ACGTGTTGGTCCATTGCTGC | [132] | ||
pmoAC | methane oxidation | methane monooxygenase | pmoC617f | ACACCTTCTGGTTCATGG | [133] |
pmoA682r | GAASGCNGAGAAGAASGC | [133] | |||
napA | nitrate reduction | periplasmic nitrate reductase | NapV16F | GCNCCNTGYMGNTTYTGYGG | [120] |
NapV17R | RTGYTGRTTRAANCCCATNGTCCA | [120] |
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Imhoff, J.F. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms 2016, 4, 19. https://doi.org/10.3390/microorganisms4020019
Imhoff JF. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms. 2016; 4(2):19. https://doi.org/10.3390/microorganisms4020019
Chicago/Turabian StyleImhoff, Johannes F. 2016. "New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment" Microorganisms 4, no. 2: 19. https://doi.org/10.3390/microorganisms4020019
APA StyleImhoff, J. F. (2016). New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms, 4(2), 19. https://doi.org/10.3390/microorganisms4020019