[en] Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants.
Research Center/Unit :
TERRA Teaching and Research Centre - TERRA
Disciplines :
Animal production & animal husbandry
Author, co-author :
Jin, Di; Institue of Animal Science - CAAS
Zhao, Shengguo; Institue of Animal Science - CAAS
Wang, Pengpeng; Institue of Animal Science - CAAS
Zheng, Nan; Institue of Animal Science - CAAS
Bu, Dengpan; Institue of Animal Science - CAAS
Beckers, Yves ; Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Zootechnie
Wang, Jiaqi; Institue of Animal Science - CAAS
Language :
English
Title :
Insights into abundant rumen ureolytic bacterial community using rumen simulation system
Publication date :
2016
Journal title :
Frontiers in Microbiology
eISSN :
1664-302X
Publisher :
Frontiers Research Foundation, Lausanne, Switzerland
NSCF - National Natural Science Foundation of China Agricultural Science and Technology Innovation Program Modern Agro-Industry Technology Research System of the PR China Terra Research Centre - AgricultureIsLife
An, D., Cai, S., and Dong, X. (2006). Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int. J. Syst. Evol. Microbiol. 56, 2043-2048. doi: 10.1099/ijs.0.64059-0.
Benini, S., Rypniewski, W. R., Wilson, K. S., Miletti, S., Ciurli, S., and Mangani, S. (2000). The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 Å resolution. J. Biol. Inorg. Chem. 5, 110-118. doi: 10.1007/s007750050014.
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, et al. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Meth. 10, 57-59. doi: 10.1038/nmeth.2276.
Broderick, G. A., and Kang, J. H. (1980). Automated simultaneous determination of ammonia and total amino acids in ruminal fluid and in vitro media. J. Dairy Sci. 63, 64-75. doi: 10.3168/jds. S0022-0302(80)82888-8.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., and Bushman, F. D. (2010). QIIME allows analysis of highthroughput community sequencing data. Nat. Methods 7, 336-336. doi: 10.1038/nmeth.f.303.
Chen, Y.-Y. M., Weaver, C. A., and Burne, R. A. (2000). Dual functions of Streptococcus salivarius urease. J. Bacteriol. 182, 4667-4669. doi: 10.1128/JB.182.16.4667-4669.2000.
Collier, J. L., Baker, K. M., and Bell, S. L. (2009). Diversity of urea-degrading microorganisms in open-ocean and estuarine planktonic communities. Environ. Microbiol. 11, 3118-3131. doi: 10.1111/j.1462-2920.2009.02016.x.
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., et al. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072. doi: 10.1128/AEM.03006-05.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. doi: 10.1093/bioinformatics/btr381.
Garcia-Delgado, G., Little, P., and Barnum, D. (1977). A comparison of various haemophilus somnus strains. Can. J. Comp. Med. 41, 380.
Goswami, D., Patel, K., Parmar, S., Vaghela, H., Muley, N., Dhandhukia, P., et al. (2015). Elucidating multifaceted urease producing marine Pseudomonas aeruginosa BG as a cogent PGPR and bio-control agent. Plant Growth Regul. 75, 253-263. doi: 10.1007/s10725-014-9949-1.
Gresham, T. L. T., Sheridan, P. P., Watwood, M. E., Fujita, Y., and Colwell, F. S. (2007). Design and validation ofurec-based primers for groundwater detection of urea-hydrolyzing bacteria. Geomicrobiol. J. 24, 353-364. doi: 10.1080/01490450701459283.
Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., et al. (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494-504. doi: 10.1101/gr.112730.110.
Hook, S. E., Steele, M. A., Northwood, K. S., Dijkstra, J., France, J., Wright, A. D., et al. (2011). Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows. FEMS Microbiol. Ecol. 78, 275-284. doi: 10.1111/j.1574-6941.2011.01154.x.
Hristov, A. N., Lee, C., Hristova, R., Huhtanen, P., and Firkins, J. L. (2012). A meta-analysis of variability in continuous-culture ruminal fermentation and digestibility data. J. Dairy Sci. 95, 5299-5307. doi: 10.3168/jds.2012-5533.
Huse, S. M., Dethlefsen, L., Huber, J. A., Welch, D. M., Relman, D. A., and Sogin, M. L. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255. doi: 10.1371/journal.pgen.1000255.
Jones, G. A., and Milligan, J. D. (1975). Influence on some rumen and blood parameters of feeding acetohydroxamic acid in a urea-containing ration for lambs. Can. J. Anim. Sci. 55, 39-47. doi: 10.4141/cjas75-006.
Jyothi, N., and Umamahe, S. (2013). Production of protease and urease by kerosene utilizing fluorescent Pseudomonads isolated from local red latirite soil. Bioscan 8, 353-357.
Kakimoto, S., Okazaki, K., Sakane, T., Imai, K., Sumino, Y., Akiyama, S. I., et al. (1989). Isolation and taxonomie characterization of acid urease-producing bacteria. Agric. Biol. Chem. 53, 1111-1117. doi: 10.1080/00021369.1989.10869439.
Kertz, A. F. (2010). Review: urea feeding to dairy cattle: a historical perspective and review. Prof. Anim. Sci. 26, 257-272. doi: 10.15232/s1080-7446(15)30593-3.
Kilian, M. (2015). "Haemophilus," in Bergey's Manual of Systematics of Archaea and Bacteria, ed W. B. Whitman (New York, NY: Springer), 1-47. doi: 10.1002/9781118960608.gbm01198.
Kim, J. N., Henriksen, E. D., Cann, I. K., and Mackie, R. I. (2014). Nitrogen utilization and metabolism in Ruminococcus albus 8. Appl. Environ. Microbiol. 80, 3095-3102. doi: 10.1128/AEM.00029-14.
Kim, M., Morrison, M., and Yu, Z. (2011). Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol. Ecol. 76, 49-63. doi: 10.1111/j.1574-6941.2010.01029.x.
Lozupone, C. A., Hamady, M., Kelley, S. T., and Knight, R. (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576-1585. doi: 10.1128/AEM.01996-06.
Lynd, L. R., Weimer, P. J., van Zyl, W. H., and Pretorius, I. S. (2002). Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. R 66, 506-577. doi: 10.1128/MMBR.66.3.506-577.2002.
Magoè, T., and Salzberg, S. L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963. doi: 10.1093/bioinformatics/btr507.
Mahnert, A., Moissl-Eichinger, C., and Berg, G. (2015). Microbiome interplay: plants alter microbial abundance and diversity within the built environment. Front. Microbiol. 6:887. doi: 10.3389/fmicb.2015.00887.
Makkar, H. P., Sharma, O. P., Dawra, R. K., and Negi, S. S. (1981). Effect of acetohydroxamic acid on rumen urease activity in vitro. J. Dairy Sci. 64, 643-648. doi: 10.3168/jds. S0022-0302(81)82624-0.
Marri, P. R., Paniscus, M., Weyand, N. J., Rendon, M. A., Calton, C. M., Hernandez, D. R., et al. (2010). Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. PLoS ONE 5:e11835. doi: 10.1371/journal.pone.0011835.
McCrea, K. W., Xie, J., LaCross, N., Patel, M., Mukundan, D., Murphy, T. F., et al. (2008). Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains. J. Clin. Microbiol. 46, 406-416. doi: 10.1128/JCM.01832-07.
Minas, K., McEwan, N. R., Newbold, C. J., and Scott, K. P. (2011). Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures. FEMS Microbiol. Lett. 325, 162-169. doi: 10.1111/j.1574-6968.2011.02424.x.
Morou-Bermudez, E., and Burne, R. A. (1999). Genetic and physiologic characterization of urease of Actinomyces naeslundii. Infect. Immun. 67, 504-512.
Morou-Bermudez, E., and Burne, R. A. (2000). Analysis of urease expression in Actinomyces naeslundii WVU45. Infect. Immun. 68, 6670-6676. doi: 10.1128/IAI.68.12.6670-6676.2000.
Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L., and Graf, J. (2014). Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS ONE 9:e94249. doi: 10.1371/journal.pone.0094249.
Oyeleke, S., and Okusanmi, T. (2008). Isolation and characterization of cellulose hydrolysing microorganism from the rumen of ruminants. Afr. J. Biotechnol. 7, 1503-1504. doi: 10.5897/AJB08.142.
Pandya, P., Singh, K., Parnerkar, S., Tripathi, A., Mehta, H., Rank, D., et al. (2010). Bacterial diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis. J. Appl. Genet. 51, 395-402. doi: 10.1007/BF03208869.
Patra, A. K. (2015). "Urea/Ammonia metabolism in the rumen and toxicity in ruminants," in Rumen Microbiology: From Evolution to Revolution, eds A. K. Puniya, R. Singh, and D. N. Kamra (New Delhi; Heidelberg; New York, NY; Dordrecht; London: Springer), 329-341.
Pope, P., Smith, W., Denman, S., Tringe, S., Barry, K., Hugenholtz, P., et al. (2011). Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333, 646-648. doi: 10.1126/science.1205760.
Rasko, D. A., Ravel, J., Økstad, O. A., Helgason, E., Cer, R. Z., Jiang, L., et al. (2004). The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res. 32, 977-988. doi: 10.1093/nar/gkh,258.
R Core Team (2013). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna. Available online at: http://www. R-project.org/.
Reed, K. E. (2001). Restriction enzyme mapping of bacterial urease genes: using degenerate primers to expand experimental outcomes. Biochem. Mol. Biol. Educ. 29, 239-244. doi: 10.1111/j.1539-3429.2001.tb00131.x.
Sakai, K., Yamauchi, T., Nakasu, F., and Ohe, T. (1996). Biodegradation of cellulose acetate by Neisseria sicca. Biosci. Biotechnol. Biochem. 60, 1617-1622. doi: 10.1271/bbb.60.1617.
Santos, E., and Thompson, F. (2014). "The Family Succinivibrionaceae," in The Prokaryotes, eds M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer and E. Stackebrandt (Berlin; Heidelberg: Springer), 639-648.
Sarda, D., Choonia, H. S., Sarode, D., and Lele, S. (2009). Biocalcification by Bacillus pasteurii urease: a novel application. J. Ind. Microbiol. Biot. 36, 1111-1115. doi: 10.1007/s10295-009-0581-4.
Schaal, K. P., and Yassin, A. A. (2015). "Actinomyces," in Bergey's Manual of Systematics of Archaea and Bacteria, ed W. B. Whitman (New York, NY: Springer), 1-112.
Shen, W., Jiang, Y., Wang, J., Bu, D., Sun, P., Jin, E., et al. (2012). Design and testing of rumen simulation system with discharging solid chime, liquid, and gas respectively. Trans. Chin. Soc. Agric. Eng. 28, 20-26. doi: 10.3969/j.issn.1002-6819.2012.03.004.
Singh, B. K., Nunan, N., and Millard, P. (2009). Response of fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil. FEMS Microbiol. Ecol. 70, 109-117. doi: 10.1111/j.1574-6941.2009.00731.x.
Su, J., Jin, L., Jiang, Q., Sun, W., Zhang, F., and Li, Z. (2013). Phylogenetically diverse ureC genes and their expression suggest the urea utilization by bacterial symbionts in marine sponge Xestospongia testudinaria. PLoS ONE 8:e64848. doi: 10.1371/journal.pone.0064848.
Šul'ák, M., Sikorová, L., Jankuvová, J., Javorski, P., and Pristaš, P. (2012). Variability of Actinobacteria, a minor component of rumen microflora. Folia Microbiol. 57, 351-353. doi: 10.1007/s12223-012-0140-7.
Upadhyay, L. S. B. (2012). Urease inhibitors: a review. Indian J. Biotechnol. 11, 381-388.
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07.
Weller, R. A., and Pilgrim, A. F. (1974). Passage of protozoa and volatile fatty acids from the rumen of the sheep and from a continuous in vitro fermentation system. Br. J. Nutr. 32, 341-351. doi: 10.1079/BJN19740087.
Williams, A., and Withers, S. E. (1983). Bacillus spp. in the rumen ecosystem. Hemicellulose depolymerases and glycoside hydrolases of Bacillus spp. and rumen isolates grown under anaerobic conditions. J. Appl. Microbiol. 55, 283-292. doi: 10.1111/j.1365-2672.1983.tb01325.x.
Wozny, M. A., Bryant, M. P., Holdeman, L. V., and Moore, W. E. (1977). Urease assay and urease-producing species of anaerobes in the bovine rumen and human feces. Appl. Environ. Microbiol. 33, 1097-1104.
Wu, S., Baldwin, R. L., Li, W., Li, C., Connor, E. E., and Li, R. W. (2012). The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA Genes. Metagenomics 1, 1-11. doi: 10.4303/mg/235571.
Zhang, R., Zhu, W., Zhu, W., Liu, J., and Mao, S. (2014). Effect of dietary forage sources on rumen microbiota, rumen fermentation and biogenic amines in dairy cows. J. Sci. Food Agric. 94, 1886-1895. doi: 10.1002/jsfa.6508.
Zhang, Y. G., Shan, A. S., and Bao, J. (2001). Effect of hydroquinone on ruminal urease in the sheep and its inhibition kinetics in vitro. Asian Aust. J. Anim. Sci. 14, 1216-1220. doi: 10.5713/ajas.2001.1216.
Zhao, S., Wang, J., Zheng, N., Bu, D., Sun, P., and Yu, Z. (2015). Reducing microbial ureolytic activity in the rumen by immunization against urease therein. BMC Vet. Res. 11:94. doi: 10.1186/s12917-015-0409-6.
Zotta, T., Ricciardi, A., Rossano, R., and Parente, E. (2008). Urease production by Streptococcus thermophilus. Food Microbiol. 25, 113-119. doi: 10.1016/j.fm.2007.07.001.
