Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms

BACKGROUND: Currently, the naïve Bayesian classifier provided by the Ribosomal Database Project (RDP) is one of the most widely used tools to classify 16S rRNA sequences, mainly collected from environmental samples. We show that RDP has 97+% assignment accuracy and is fast for 250 bp and longer reads when the read originates from a taxon known to the database. Because most environmental samples will contain organisms from taxa whose 16S rRNA genes have not been previously sequenced, we aim to benchmark how well the RDP classifier and other competing methods can discriminate these novel taxa from known taxa. PRINCIPAL FINDINGS: Because each fragment is assigned a score (containing likelihood or confidence information such as the boostrap score in the RDP classifier), we "train" a threshold to discriminate between novel and known organisms and observe its performance on a test set. The threshold that we determine tends to be conservative (low sensitivity but high specificity) for naïve Bayesian methods. Nonetheless, our method performs better with the RDP classifier than the other methods tested, measured by the f-measure and the area-under-the-curve on the receiver operating characteristic of the test set. By constraining the database to well-represented genera, sensitivity improves 3-15%. Finally, we show that the detector is a good predictor to determine novel abundant taxa (especially for finer levels of taxonomy where novelty is more likely to be present). CONCLUSIONS: We conclude that selecting a read-length appropriate RDP bootstrap score can significantly reduce the search space for identifying novel genera and higher levels in taxonomy. In addition, having a well-represented database significantly improves performance while having genera that are "highly" similar does not make a significant improvement. On a real dataset from an Amazon Terra Preta soil sample, we show that the detector can predict (or correlates to) whether novel sequences will be assigned to new taxa when the RDP database "doubles" in the future

Perspectives on Bivalves Providing Regulating Services in Integrated Multi-Trophic Aquaculture

The concept of integrating species into one culture system originates from Asia and the Middle East. Development of integrated aquaculture involving marine bivalves is relatively new, going back to the late 1980s in China and 1990s in the Western world. In this chapter, we present four cases of integrated multi-trophicaquaculture (IMTA) where bivalves are involved in providing regulating services: i) shrimp culture in ponds, ii) cascading pond systems, iii) open-water caged finfish culture and iv) bay-scale culture systems. The bay-scale integratedculture system in Sanggou Bay in China represents commercial IMTA where arange of different regulating services are provided by the bivalves. Bivalves usedegraded fragments derived from cultured kelp and organic waste products fromfish farming, and play an important role in the ecosystem processes of the bay. The provision of regulating services in shrimp and cascading ponds is evident as the system configurations allow for biogeochemical processing of waste to maximize extraction by the bivalves. The current configurations used in open-water finfish cage culture suggest that adaptation of concepts allowing for control of effluent water, producing longer contact times and increased biogeochemical processing of the waste products, will dominate future IMTA development. If global bivalve culture production is sustained, we will likely see more regulating services from bivalves in IMTA systems, as new opportunities may arise for developing novel IMTA configurations and concept