Paracoccaceae

Paracoccaceae
Colonies of Paracoccus yeei
Scientific classification Edit this classification
Domain: Bacteria
Kingdom: Pseudomonadati
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Rhodobacterales
Family: Paracoccaceae
Liang et al. 2022

The Paracoccaceae are a family of bacteria. The family comprises bacteria that are often found in marine habitats and shows great metabolic and ecological diversity. Species also occur in other habitats, such as fresh water, soil (e.g. species of Paracoccus) or wastewater (Amaricoccus). Some depend on oxygen, i.e. they are strictly aerobic. Others are facultatively anaerobic, meaning they also grow in the absence of oxygen. Many species can use photosynthesis. Some members were formerly assigned to the family Rhodobacteraceae. That family was dissolved and its genera were distributed among several families.

Characteristics

The members of the family Paracoccaceae are Gram-negative bacteria, which means that they stain red or pink in the Gram stain. They can occur in various shapes, including coccoid (spherical) and rod-shaped.

Some members are flagellated and motile; non-flagellated representatives, such as Methylarcula, also exist. Some species reproduce by budding. Instead of the binary fission typical of most bacterial species, in which two cells of more or less the same shape and size are formed, an initially smaller daughter cell forms and remains attached to the mother cell for some time. The daughter cell does not grow uniformly but in a polar manner, at one specific point. The budding species include, for example, Rhodobacter blasticus and Gemmobacter aquatilis.

Metabolism

The Paracoccaceae are characterised by a versatile metabolism. Many species are able to use a wide range of organic compounds under aerobic and anaerobic conditions. Methylotrophic species, which use e.g. methylamine to obtain energy, are also present.

Several species are photoheterotrophic, i.e. they use light energy and additionally require organic compounds. Photoautotrophic bacteria are also present.

The phototrophic species possess bacteriochlorophyll a and belong to the purple non-sulfur bacteria. They mostly use hydrogen sulfide (H2S) as an electron donor, releasing sulfur as a product. Some species can then oxidise the sulfur further to sulfate and thereby gain energy once more. These include many species of Rhodobacter. Some species of the genus Roseinatronobacter possess relatively rare carotenoids known as demethylspheroidene and demethylspheroidenone.

Some species, e.g. many of Rhodobacter, are in addition able to grow photolithoautotrophically. For this they use reduced sulfur compounds (such as sulfide or thiosulfate) or hydrogen as electron donors and bicarbonate (when in water) or CO2 as the carbon source for building cell material; these compounds are fixed via the Calvin cycle.

Some genera are so-called "aerobic anoxygenic phototrophic bacteria" (AAPs). These organisms can carry out photosynthesis under aerobic conditions; however, carbon dioxide is not used in the process, and so they do not produce oxygen. They use light as an additional energy source, and organic substances are required as well. These include, for example, some species of Roseinatronobacter. Some are strictly heterotrophic bacteria. Some are also able to use sulfur compounds autotrophically. Denitrifying species are also present. To obtain energy, they convert the nitrogen bound in nitrate (NO3−) to molecular nitrogen (N2). Paracoccus denitrificans is a model organism for the study of denitrification. Such bacteria play a role in the nitrogen cycle. Some species are also able to use aromatic hydrocarbons in their metabolism and thus degrade them.

The species Rhodobacter capsulatus (also referred to as Cereibacter sphaeroides) produces so-called "gene transfer agents" (GTAs). These are virus-like particles that are produced by the bacterium and can transfer genetic material between cells. Only a very small, random segment of the DNA is transferred. This results in horizontal gene transfer, which plays an important role in evolution. GTAs presumably arose from former temperate phages. Over time, the viruses lost the ability to replicate independently and became permanently integrated into the host cell.

Some species accumulate polyhydroxybutyrate (PHB) or various other polyhydroxyalkanoates (PHA), which serve as a reserve for periods of nutrient scarcity.

The following is a table of some example species:

Species of the family Paracoccaceae
SpeciesIsolation/habitatMetabolismNa⁺ requirementOther notesReferences
Defluviimonas denitrificansBiofilter, marine aquaculture recirculation systems (Israel)chemoorganoheterotrophicNo-Foesel et al., 2011
Gemmobacter aquatilisPond (USA)facultatively anaerobic chemoorganoheterotrophic, denitrification under anaerobic conditions No-Rothe et al., 1987
Gemmobacter changlensisSnow, Himalayas (India)photoheterotrophic (PH)Noformerly Rhodobacter changlensisChen et al., 2013a; Anil Kumar et al., 2007
Haematobacter missouriensis clinical blood samples from wounds aerobic chemoorganotrophic No - Helsel et al. 2007
Methylarcula marina an estuary of the Sea of Azov, Russia FMT Yes produces ectoine Doronina et al. 2000
Paracoccus denitrificans soil, wastewater, liquid manure, sewage sludge facultatively chemolithoautotrophic No capable of denitrification Ludwig et al. 1993
Pararhodobacter aggregans in the biofilter of a marine aquaculture, Israel aerobic, chemoorganotrophic No -
Pseudorhodobacter ferrugineus biofilter of a marine aquaculture aerobic, chemoorganotrophic No -
Rhodobacter capsulatusstagnant fresh water, exposed to light, with reduced oxygen (USA, Cuba)purple non-sulfur bacteria No-Imhoff et al., 1984
Rhodobacter vinaykumariitidal seawater (India)purple non-sulfur bacteriaYes-Srinivas et al., 2007a
Rhodobacter viridisriver water and mud (India)purple non-sulfur bacteriaNo-Shalem Raj et al., 2013
Roseinatronobacter thiooxidans soda lake in Siberia aerobic anoxygenic phototroph Yes - Sorokin et al. 2000
Roseitranquillus sediminis sediment of Kongsfjorden, Ny-Ålesund, Svalbard chemoorganoheterotrophic Yes - Umar et al., 2021
Solirhodobacter olei oil-contaminated soil from the Daqing oil field in China chemolithoautotrophic with thiosulfate No - Chu et al. 2020
Thioclava pacifica in the vicinity of a sulfide-rich hydrothermal vent on the coast of Papua New Guinea chemolithoautotrophic growth with sulfur compounds Yes - Sorokin et al. 2005
Zongyanglinia marinus from sediment in the Yellow Sea strictly aerobic, reduces nitrate to N2 Yes - Chu et al. 2020

Abbreviations:

Ecology

The Paracoccaceae occur in a wide variety of environments, including soil, fresh water and marine ecosystems. Their metabolic flexibility allows them to adapt to different ecological niches. Some occur in extreme environments. Species such as Roseinatronobacter bogoriensis and R. thiooxidans have been found in soda lakes. Other strains inhabit sulfidic hydrothermal areas (e.g. Thioclava pacifica) and hot springs (Pleomorphobacterium xiamenense).

Applications

Members of the family Paracoccaceae have potential for biotechnological applications such as bioremediation and wastewater treatment. Through their denitrification capabilities they could contribute to the removal of nitrate from polluted ecosystems.

Taxonomy

In 2022 the family Rhodobacteraceae was dissolved on the basis of genetic studies. On the basis of taxonomic studies, such as comparisons of ribosomal RNA, its members were distributed among the new families Roseobacteraceae, Stappiaceae, Ahrensiaceae and the Paracoccaceae. The genus Rhodobacter, which gave the original family its name, was placed in the Paracoccaceae.

The following is a list of some genera (as of December 2024):

References

  1. 1 2 3 Liang, Kevin Y. H.; Orata, Fabini D.; Boucher, Yann F.; Case, Rebecca J. (2021). "Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the "roseobacter clade" into a novel family, Roseobacteraceae fam. nov". Frontiers in Microbiology. 12 683109. doi:10.3389/fmicb.2021.683109. ISSN 1664-302X. PMC 8267831. PMID 34248901.
  2. 1 2 3 4 Göker, Markus (2022). "Filling the gaps: missing taxon names at the ranks of class, order and family". International Journal of Systematic and Evolutionary Microbiology. 72 (12): 005638. doi:10.1099/ijsem.0.005638. PMID 36748602. Retrieved 13 October 2026.
  3. 1 2 3 Zhaobin Huang, Meiqin Li, Aharon Oren, Qiliang Lai (2024-04-30). "Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat". Frontiers in Microbiology. 15 1376777. doi:10.3389/fmicb.2024.1376777. ISSN 1664-302X. PMC 11092380. PMID 38746742.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ↑ Gaimster, Hannah; Alston, Mark; Richardson, David J; Gates, Andrew J; Rowley, Gary (2017-12-20). "Transcriptional and environmental control of bacterial denitrification and N2O emissions". FEMS Microbiology Letters. 365 (5). doi:10.1093/femsle/fnx277. ISSN 1574-6968. PMID 29272423.
  5. ↑ Gates, Andrew J.; Luque-Almagro, Victor M.; Goddard, Alan D.; Ferguson, Stuart J.; Roldán, M. Dolores; Richardson, David J. (2011-05-01). "A composite biochemical system for bacterial nitrate and nitrite assimilation as exemplified by Paracoccus denitrificans". Biochemical Journal. 435 (3): 743–753. doi:10.1042/BJ20101920. ISSN 0264-6021. PMID 21348864.
  6. 1 2 Asif Hameed, Kokkarambath Vannadil Suchithra, Shih-Yao Lin, Paul Stothard, Chiu-Chung Young (November 2023). "Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-ET affiliated to family Paracoccaceae". Antonie van Leeuwenhoek. 116 (11): 1247–1259. doi:10.1007/s10482-023-01881-6. ISSN 0003-6072. PMID 37740842.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ↑ Georg Fuchs (2017). Allgemeine Mikrobiologie (in German) (10th, unrevised ed.). Stuttgart: Thieme. ISBN 978-3-13-241885-1.
  8. ↑ Andrew S. Lang, Alexander B. Westbye, J. Thomas Beatty (2017-09-29). "The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange". Annual Review of Virology. 4 (1): 87–104. doi:10.1146/annurev-virology-101416-041624. ISSN 2327-056X. PMID 28784044. Retrieved 2024-12-30.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. 1 2 3 4 María J. Pujalte, Teresa Lucena, María A. Ruvira, David Ruiz Arahal, M. Carmen Macián (2014). "The Family Rhodobacteraceae". The Prokaryotes. Berlin, Heidelberg: Springer Berlin Heidelberg. pp. 439–512. doi:10.1007/978-3-642-30197-1_377. ISBN 978-3-642-30196-4.{{cite book}}: CS1 maint: multiple names: authors list (link)
  10. ↑ Doronina NV, Trotsenko YA (2000): A novel plant-associated thermotolerant alkaliphilic methylotroph of the genus Paracoccus. Microbiology vol. 69; pp. 593–598
  11. ↑ Imhoff JF, Truper HG, Pfenning N (1984): Rearrangement of the species and genera of the phototrophic "purple nonsulfur bacteria". In: Int J Syst Bacteriol vol. 34: pp. 340–34
  12. ↑ Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Imhoff JF (2007a): Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter. In: Int J Syst Evol Microbiol vol. 57: pp. 1984–1987
  13. ↑ Shalem Raj P, Ramaprasad EVV, Vaseef S, Sasikala C, Ramana CV (2013): Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from Western Ghats of India. In: Int J Syst Evol Microbiol vol. 63: pp. 181–186
  14. ↑ Umar M, Krishnan KP, Sinha RK, Kannukkarathi T, Merlin TS, Johnson JI, Joseph V, Puthiyedathu ST.: Roseitranquillus sediminis gen. nov., sp. nov. a novel genus and species of the family Rhodobacteraceae, isolated from sediment of an Arctic fjord. In: Antonie Van Leeuwenhoek 2021; vol. 114, pp. 2147–2162. doi:10.1007/s10482-021-01669-6
  15. ↑ Rothe, B., Fischer, A., Hirsch, P. et al.: The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen., nov. sp. nov. In: Arch. Microbiol. vol. 147, 92–99 (1987). doi:10.1007/BF00492911
  16. ↑ Chen W-M, Cho N-T, Huang W-C, Young C-C, Sheu S-Y (2013): Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and Gemmobacter aquatilis. In: Int J Syst Evol Microbiol vol. 63, pp. 470–478
  17. ↑ Sorokin DY, Tourova TP, Kuznetsov BB, Bryantseva IA, Gorlenko VM (2000): Roseinatronobacter thiooxidans gen. nov., sp. nov., a new alkaliphilic aerobic bacteriochlorophyll a-containing bacterium isolated from a soda lake. In: Mikrobiologiya vol. 69, pp. 89–97 (in Russian)
  18. ↑ Helsel LO, Hollis D, Steigerwalt AG, Morey RE, Jordan J, Aye T, Radosevic J, Jannat-Khah D, Thiry D, Lonsway DR, Patel JB, Daneshvar MI, Levett PN 2007. Identification of "Haematobacter," a New Genus of Aerobic Gram-Negative Rods Isolated from Clinical Specimens, and Reclassification of Rhodobacter massiliensis as "Haematobacter massiliensis comb. nov.". J Clin Microbiol 45. doi:10.1128/jcm.01188-06
  19. 1 2 Sorokin DY, Tourova TP, Spiridonova EM, Rainey FA, Muyzer G (2005a) Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area. Int J Syst Evol Microbiol 55:1069–1075
  20. ↑ Chu C, Liu B, Lian Z, Zheng H, Chen C, Yue Z, Li L, Sun Z.: Solirhodobacter olei gen. nov., sp. nov., a nonphotosynthetic bacterium isolated from oil-contaminated soil. In: Int J Syst Evol Microbiol 2020; vol. 70, pp. 582–588
  21. ↑ Xu, L., Liu, A. & Zhang, YJ. Zongyanglinia huanghaiensis gen. nov., sp. nov., a novel denitrifying bacterium isolated from the yellow sea, and transfer of Pelagicola marinus to Zongyanglinia gen. nov. as Zongyanglinia marinus comb. nov. Antonie van Leeuwenhoek 114, 137–149 (2021). doi:10.1007/s10482-020-01507-1
  22. ↑ Foesel BU, Drake HL, Schramm A (2011): Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., nonphototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. In: Syst Appl Microbiol vol. 34: pp. 498–502, doi:10.1016/j.syapm.2011.08.006
  23. ↑ Xinli Pan, Zhe Li, Fei Li, Yuanlin Huang, Qiaozhen Wang, Shushi Huang, Wenjin Hu, Mingguo Jiang (November 2021). "Thermohalobaculum xanthum gen. nov., sp. nov., a moderately thermophilic bacterium isolated from mangrove sediment". Antonie van Leeuwenhoek. 114 (11): 1819–1828. doi:10.1007/s10482-021-01641-4. ISSN 0003-6072. PMID 34424448.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  24. ↑ Decui Yin, Liwei Chen, Jingqun Ao, Chunxiang Ai, Xinhua Chen (2013-05-01). "Pleomorphobacterium xiamenense gen. nov., sp. nov., a moderate thermophile isolated from a terrestrial hot spring". International Journal of Systematic and Evolutionary Microbiology. 63 (Pt_5): 1868–1873. doi:10.1099/ijs.0.042713-0. ISSN 1466-5026. PMID 23041633.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  25. ↑ Hördt, Anton; López, Marina García; Meier-Kolthoff, Jan P.; Schleuning, Marcel; Weinhold, Lisa-Maria; Tindall, Brian J.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Göker, Markus (2020). "Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria". Frontiers in Microbiology. 11 468. Bibcode:2020FrMic..1100468H. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
  26. ↑ "Family Rhodobacteraceae". List of Prokaryotic names with Standing in Nomenclature. DSMZ. Retrieved 13 October 2026.
  27. ↑ "Family Paracoccaceae". List of Prokaryotic names with Standing in Nomenclature. DSMZ. Retrieved 13 October 2026.

Further reading