For many years, the generation of nitrates from organic sources in order to create nutrient solutions for hydroponics had proved a challenge until lately when microorganisms were introduced to perform this task. The objectives of the current study therefore were to use local microbial consortium to nitrify goat manure in water and to determine microbial diversity in the inoculated consortium. Therefore, microorganisms were sourced from garden soil and natural compost at the Sam Nujoma Marine resources Research Centre (SANUMARC) in Henties Bay Namibia to convert organic nitrogen in goat manure from Utuseb farm near Walvis Bay into nitrates. Results show that microbial consortium from the compost source produced significantly (P< 0.05) more nitrates followed by the garden-soil source, suggesting that it is necessary to add inoculum in order to generate nitrate from goat manure. The ammonia oxidising bacteria (AOB) community from the compost sample’s was dominated by uncultured ammonia-oxidising species followed by uncultured bacterium (both not identified), with the least being Nitrosomonas species. The AOB community from the garden source was dominated by uncultured bacterium, followed by uncultured ammonia-oxidising species and the least being Nitrosomonas species. NOB community from the compost source was dominated by uncultured bacterium, followed by Nitrobacter winogradskyi and Nitobacter vulgaris with the least being Nitrococcus mobilis and Nitrospira moscovensis. For the garden soil microbial source, uncultured nitrite-oxidising bacteria dominated followed by uncultured bacterium, whereas the least species were N. moscovensis and Nitrobacter alkalicus. Moreover, community composition of the compost sample was more diverse than the community from the garden sample. These results maintain that there are other unculturable yet important microbes doing the same job if not better than the known ones, in this case suggesting that there may be other local nitrite-oxidizing bacteria responsible for oxidizing ammonia other than the traditionally known Nitrobacter, Nitrospira and Nitrococcus species.
Key words: Organic hydroponics, ammonification, nitrification, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria.