Towards an operational SAR-based rice monitoring system in Asia: Examples from 13 demonstration sites across Asia in the RIICE project

Rice is the most important food security crop in Asia. Information on its seasonal extent forms part of the national accounting of many Asian countries. Synthetic Aperture Radar (SAR) imagery is highly suitable for detecting lowland rice, especially in tropical and subtropical regions, where pervasive cloud cover in the rainy seasons precludes the use of optical imagery. Here, we present a simple, robust, rule-based classification for mapping rice area with regularly acquired, multi-temporal, X-band, HH-polarized SAR imagery and site-specific parameters for classification. The rules for rice detection are based on the well-studied temporal signature of rice from SAR backscatter and its relationship with crop stages. We also present a procedure for estimating the parameters based on temporal feature descriptors that concisely characterize the key information in the rice signatures in monitored field locations within each site. We demonstrate the robustness of the approach on a very large dataset. A total of 127 images across 13 footprints in six countries in Asia were obtained between October 2012, and April 2014, covering 4.78 m ha. More than 1900 in-season site visits were conducted across 228 monitoring locations in the footprints for classification purposes, and more than 1300 field observations were made for accuracy assessment. Some 1.6 m ha of rice were mapped with classification accuracies from 85% to 95% based on the parameters that were closely related to the observed temporal feature descriptors derived for each site. The 13 sites capture much of the diversity in water management, crop establishment and maturity in South and Southeast Asia. The study demonstrates the feasibility of rice detection at the national scale using multi-temporal SAR imagery with robust classification methods and parameters that are based on the knowledge of the temporal dynamics of the rice crop. We highlight the need for the development of an open-access library of temporal signatures, further investigation into temporal feature descriptors and better ancillary data to reduce the risk of misclassification with surfaces that have temporal backscatter dynamics similar to those of rice. We conclude with observations on the need to define appropriate SAR acquisition plans to support policies and decisions related to food security

Isolation, Molecular Characterization and Virulence Study (Pathogenesis) of Photobacterium damselae subsp. damselae Isolated from Sea-cage and Wild Fishes

Background: Photobacterium damselae subsp. damselae is one of the most devastating zoonotic bacterial pathogen affects both fish and human health worldwide. The study aims to isolate and characterize P. damselae subsp. damselae from both wild caught and cage culture fishes. The virulence potential of P. damselae subsp. damselae on damselfish also been revealed.Methods: A total of 212 finfishes from cage culture and wild environment were collected from the south east coast of India and identified for the presence of zoonotic P. damselae subsp. damselae. Standard biochemical and molecular methods (using specific gene) were employed to identify the P. damselae subsp. damselae isolates. A total of 61 isolates were identified as P. damselae subsp. damselae. Dendogram analysis was done for selected 30 strains based on band thickness of PCR product after using IS and ERIC PCR. The data were statistically analysed by unweighted pair group method using mathematic averages (UPGMA) for numerical analysis of banding patterns. The thirty out of sixty one isolates (20% or 50%) showed their presence in both wild caught and cage cultured fishes. The isolates from the wild caught fish were tested for their virulence on damsel fish and histopathological effect also studied. Result: High prevalence of P. damselae subsp. damselae in wild caught parrot fish was noticed when compared to the cage culture fishes. The dendrogram obtained after numerical analysis with the Dice coefficient and UPGMA method shows that all patterns shared more than 50% similarity. Experimental challenge revealed that P. damselae subsp. damselae isolates from wild caught will cause severe tissue damage, abnormal behavior, clinical signs and also leads to fish mortality.</jats:p

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Not AvailableBackground: Photobacterium damselae subsp. damselae is one of the most devastating zoonotic bacterial pathogen affects both fish and human health worldwide. The study aims to isolate and characterize P. damselae subsp. damselae from both wild caught and cage culture fishes. The virulence potential of P. damselae subsp. damselae on damselfish also been revealed. Methods: A total of 212 finfishes from cage culture and wild environment were collected from the south east coast of India and identified for the presence of zoonotic P. damselae subsp. damselae. Standard biochemical and molecular methods (using specific gene) were employed to identify the P. damselae subsp. damselae isolates. A total of 61 isolates were identified as P. damselae subsp. damselae. Dendogram analysis was done for selected 30 strains based on band thickness of PCR product after using IS and ERIC PCR. The data were statistically analysed by unweighted pair group method using mathematic averages (UPGMA) for numerical analysis of banding patterns. The thirty out of sixty one isolates (20% or 50%) showed their presence in both wild caught and cage cultured fishes. The isolates from the wild caught fish were tested for their virulence on damsel fish and histopathological effect also studied. Result: High prevalence of P. damselae subsp. damselae in wild caught parrot fish was noticed when compared to the cage culture fishes. The dendrogram obtained after numerical analysis with the Dice coefficient and UPGMA method shows that all patterns shared more than 50% similarity. Experimental challenge revealed that P. damselae subsp. damselae isolates from wild caught will cause severe tissue damage, abnormal behavior, clinical signs and also leads to fish mortality.Not Availabl

Experimental Infection of Goldfish (Carassius auratus L.) and Tilapia (Oreochromis niloticus L.) with Koi Ranavirus (KIRV)

Background: Ranaviruses are now emerging as serious pathogens for the amphibians, reptiles and fishes. The aim of this study was the determination of the susceptibility of goldfish (Carassius auratus L.) and tilapia (Oreochromis niloticus L.) to experimental infection with Koi ranavirus (KIRV). Methods: The experimental fishes were challenged with an infective dose of KIRV (106.8 TCID50/ml) by intraperitoneal injection (IP), while the control groups were injected with L-15 medium. Target tissues were collected from the experimental fishes infected with virus at 3, 7, 14, 21 and 28 dpi. Tissue samples were subjected to detection of KIRV by polymerase chain reaction (PCR), cell culture assay and histopathological technique. Result: This study reports no specific clinical signs and mortality due to virus infection during the experimental period. Experimentally infected goldfish and tilapia were tested positive for KIRV by PCR at 3 dpi, while target viral DNA was also detected in tilapia at 7 dpi by PCR. However, specific DNA of KIRV was not detected in tissues of experimental fish sampled at later experimental study periods. Cell culture assay revealed no cytopathic effect in the Epithelioma Papulosum Cyprini (EPC) cell line at all sampling time points. Histopathological study revealed focal necrosis, shrunken glomerulus and detached epithelium of tubules in kidney tissue at 3 and 7 dpi in gold fish and melanomacrophage cells and focal necrosis of glomerulus and detachment of the epithelium of tubules in kidney tissue at 3 and 7 dpi in tilapia. Melanomacrophage centers and necrosis were observed in spleen tissues of goldfish and tilapia at 3 and 7 dpi. The challenge study indicated that goldfish and tilapia are not the targeted species for KIRV. </jats:p

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Not AvailableHeavy mortality in cage farmed cobia in the southeast coast of Tamil Nadu occurred during the summer of 2016 was investigated. About 60 per cent of the fish died following a few days of high temperature and low wind in the coastal region. The fish had an average size of 27.5 cm length and 200 g weight. The affected fish had focal erythematous lesions on the ventral distended abdomen, peritoneal serosanguinous fluid accumulation, splenomegaly and swollen kidney. Bacteriological examination of the peritoneal fluid, kidney and spleen revealed the presence of Gram negative short rods in large numbers. The bacteria grew as green colonies on thiosulphate citrate bile salt sucrose agar. The tissues were also screened for the presence of nervous necrosis nodavirus by PCR and cell culture but did not yield positive result. The bacterial strains isolated from the tissues were identified as Photobacterium damselae sub sp. damselae using API 20 E microbial identification kit. The species was confirmed by multiplex PCR for 16S rRNA and urease gene. Sequence analysis of 16S rRNA showed 99 per cent homogeneity with P. damselae subsp. damselae. One of the isolates was used for the pathogenicity study in sea bass fingerlings. The experimental infection was done by intraperitoneal administration of 50 micro liters of two dilutions of the culture at 4.2 ×10 raised to the power 5 and 4.2×103 cfu per fish. The experiment revealed that the bacteria were highly pathogenic to seabass and could induce 100 per cent mortality in 36 h. The same bacteria were re-isolated from kidney sample of moribund fish and were confirmed as Pdd with API test kits and 16S rRNA sequencing. The isolates were also screened for the presence of virulence genes.Not Availabl