A direct approach for identifying predators is visual identification of prey remains in predators’ guts or feces . While visual identification of prey gut contents can sometimes yield the necessary taxonomic resolution to identify insect pests, the necessary inspection labor is considerable and sampling techniques often result in high mortality rates among study subjects. Molecular identification techniques, however, offer great potential to yield insight into predator–prey interactions . These techniques often rely on targeting and sequencing a standardized DNA region across species to facilitate identifications . Applications of this approach are diverse; for example, detecting diet shifts in ancient humans , characterizing biological communities in hydrothermal vents , identifying illegal trade in endangered species , and surveying rare mammals with DNA from leeches . Similarly, molecular identification in feces,regurgitate, and stomach contents from carnivores, insectivores, and herbivores of diverse taxa has been used to infer diet . While the application of molecular diet analysis is becoming widespread, the technique is not without limitations. First, predators vary in gut retention times and digestion processes, which may affect detection rates and complicate comparisons among species . Second, DNA assays can misattribute diet in the presence of intraguild predation— that is, if the DNA of the prey of an intermediate predator is found in the fecal samples of a top predator . Finally, digestion degrades prey DNA, making fecal analysis more sensitive than other PCR procedures to DNA quantity . Despite these shortcomings, large pots plastic several studies have used molecular techniques to identify suites of pest predators, largely through DNA analysis of arthropod predators’ gut contents .
Less work has focused on vertebrate insectivores, despite their great potential to control pest infestations . Those that have studied vertebrate predators of insect pests tend to analyze single predator species rather than communities . Further, analyses have neglected the biologically diverse, tropical countries that may stand to benefit most from conservation-minded pest-management plans . We used molecular fecal analysis to identify bird predators of coffee’s most damaging insect pest— the coffee berry borer beetle . Coffee is cultivated across the tropics, with a total export value over US$20 billion and twenty million households involved in its production . The borer has invaded almost every coffee-producing country in recent years. In fact, the borer invaded Costa Rica in 2000 and our study sites in 2005. It spends the majority of its life cycle within coffee berries, overwintering in unharvested berries and undergoing a major dispersal event several months after the first rains . Previous exclusion experiments have shown that birds consume the borer, likely during the primary dispersal event or secondary movements to adjacent berries throughout the year . The borer’s small size makes directly witnessing predation unlikely . Our work builds on Karp et al. , which used exclosures to quantify bird-mediated borer control. Here, we sought to characterize more completely which species are borer predators, supplementing their analysis with an additional 961 fecal samples and 33 bird species . In addition, we verified this approach through feeding trials with three insectivorous bird species. Finally, we compiled a database of bird conservation and functional traits to make a preliminary determination of the traits associated with borer consumption and to assess whether species that important for controlling damaging insect pests are also conservation targets.
We assessed whether confirmed borer predators shared functional traits through compiling a trait database for birds in our study area, focusing on resource and acquisition traits that may affect pest-control provision . We used measurements from birds we captured, and a bird population dynamics dataset collected at 18 nearby sites . Wing chord length and mass were obtained from the population dynamics dataset. We also calculated the total number of captures for each species. We collected bill width , bill length , and tarsus length from species that we trapped during fecal sample collection. Body lengths were obtained from literature . We gathered behavioral traits from literature . We translated foraging stratum into an ordinal scale , and calculated the average foraging stratum for each species. We quantified diet breadth as the number of food categories consumed . From literature and conversations with local ornithologists , we also identified species that consumed insects and the subset that specialized strictly on insects.Ecosystem-service management necessitates identifying service providers, especially in the many agricultural systems that are rapidly expanding and intensifying . Our analysis of ~1500 fecal samples documented that six Costa Rican bird species consume coffee’s most damaging insect pest. Still, detection rates were very low: only 0.7% of analyzed samples contained borer DNA. We offer several explanations for low detection. First, we sampled the entire bird community, including frugivores which do not likely consume the borer. Second, borer abundance is low in our study system. Only 2.5% of berries across plantations are currently infested with borers, whereas infestation has soared above 90% in other countries . Third, detection windows may be narrow. We detected borer DNA in only one sample defecated within 30 min of feeding. Insect DNA could be detected in Carrion Crow feces 30 minutes to 4 hours after consumption .
Borers disperse most often and hence are most vulnerable to predation in the afternoon . Because tropical weather constraints precluded afternoon sampling, a mismatch in sampling and consumption could have depressed detections. Finally, feeding trials demonstrated that false negatives are regular. Models predicted that a positive detection was ~20 times more likely when birds were fed 8 borers and defecated 0.1 g versus 2 borers and 0.01 g. In addition to DNA degradation in the gut, our extraction and PCR procedures may be prone to false negatives. First, PCR inhibitors can persist through extraction and impede DNA amplification from fecal pellets . Second, unlike the primers developed by Jaramillo et al. , the primers that we developed were not specific to the berry borer, meaning the primers could have amplified DNA from any one of the many species of insects that a bird had recently consumed. Moreover, iterant non-specific PCR binding of either primer set could generate chimeric sequences of multiple species. Accordingly, only 10 of the 57 samples that yielded PCR products of the expected size range were identified as borer DNA after sequencing. Future work could utilize a post-PCR sorting method such as next generation sequencing or cloning to help reduce the frequency of false negatives . Low detection rates suggest that there are other species that consume the borer that we did not identify. The species we did identify, however, shared traits that may be characteristic of these other predators. All identified borer predators except the nectarivorous White-tailed Emerald were strict insectivores. Unsurprising given the borer’s size , borer predators had narrow bills. Additionally, these species had short wings, ideal for navigating the dense coffee understory . It is possible that functional traits would change with a larger sample of predators; however, confirmed borer predators in Jamaican coffee plantations shared many of these traits , supporting our hypothesis that they may help predict other predators . A key difference between our studies, however, is that only one of the species that we identified as a borer predator is migratory . We collected our fecal samples during the period of maximum borer dispersal , a time when most migratory species are absent from Costa Rica. Because migratory species could consume borers during their secondary dispersals that occur throughout the year, square planter pots future work should temporally expand sampling effort to ensure that migratory species are well represented. Our work yielded the critical management insight that managing the predators of crop pests may require looking beyond traditional conservation targets. The six documented borer predators were not rare, endemic, or listed on the IUCN red list. Traditional conservation efforts for threatened species often center on delineating large protected areas. Focusing conservation explicitly in agricultural landscapes could benefit species involved in providing critical ecosystem services to farmers . By confirming that birds consume pests, our work could thus help change attitudes towards biodiversity in human-dominated landscapes by fostering greater recognition of its role in supporting human well being. Species interactions play a pivotal role in many ecologically and economically important ecosystem processes. Uncovering the basic relationships between animals and their food is critical for managing pest control, pollination, seed dispersal, and sanitation . Molecular methods can provide us with a window into these interactions, in some instances for the very first time. Our results demonstrate how identifying just a few key interactions between predators and their prey can yield potential insights for management. Indeed, managing nature to enhance both biodiversity and human wellbeing requires diverse approaches.
Techniques and practices have already been borrowed from fields as diverse as agronomy, economics, hydrology, psychology, and sociology. Our results indicate that molecular biology offers ecologists the ability to expand their toolkit in key dimensions and, in turn, advance ecosystem service management.California is the leading producer of table grapes. In 2019 table grapes accounted for 130,000 acres of the 918,000 acres of grapes grown in the state, with 6,588 acres grown with the variety Redglobe . The cultivar Redglobe is a variety popular for export markets, including China and Mexico, because of its flavor and long shelf life . Brown spot can cause major post harvest fruit loss in Redglobe and other late-harvest cultivars such as Crimson Seedless and Autumn King . No reliable control of brown spot has been found. A study by Swett et al. showed 100% of Redglobe clusters collected from a commercial field in Delano, in the San Joaquin Valley, had latent infections of Cladosporium species responsible for brown spot disease. Redglobe clusters may be stored for 2 to 3 months before they are shipped to Asia. When symptomless berries are in cold storage conditions for long periods, brown spot disease begins to emerge and spread . While initial infections occurin the field, once in post-harvest, infection can also easily spread from berry to berry through epidermis contact with no wounding necessary and in temperatures as low as −2°C . Attempts to manage brown spot have relied on strategies developed for the control of gray mold, a severe post harvest disease caused by the fungus Botrytis cinerea . Gray mold and brown spot have similar biology, such as infection timing, occurrence of a latency period and timing of symptoms expression . However, the common practice of using 100 to 200 parts per million per hour sulfur dioxide treatments used to control gray mold during cold storage and during transport has not been effective for the control of brown spot . Brown spot has been attributed to several species of the Cladosporium herbarum species complex and C. cladosporioides . As described by Swett et al. , typically a fluffy, light green to white mycelial mat will form where infection has taken place on the berry epidermis. A mycelial callus can form under the epidermis as a result of an internal infection, creating a scab and a brown spot on the underside of the epidermis. As the infection progresses, the scab will encompass the seed of the grape, forming a fungal fruiting body that eventually replaces the grape seed placenta, and prolific sporulation will occur on the seed . In the last 20 years, a total utilization technique for fumigant applications of SO2 during cold storage has been established for table grapes; it increases efficiency, reduces environmental pollution and protects operators . An important step of the technique is to apply the first SO2 treatment during the initial forced-air cooling of the grapes after harvest, which is then followed by weekly applications during cold storage with homogenous air distribution . The total utilization technique system uses ~ 10 times less SO2 than the previous standard fumigation system, but it requires uniform room air distribution for the treatment to be effective . The total utilization technique was based on laboratory studies that revealed that at least 100 ppm-h SO2 was necessary to kill B. cinerea conidia and inactivate exposed mycelia at 0°C . Even less than 100 ppm-h was effective at warm temperatures to cause the death of conidia and mycelium of B. cinerea on grape . These latter studies confirmed that SO2 applied at 200 ppm-30 min, 400 ppm-15 min, 50 ppm-2 h or 25 ppm-4 h was as effective as the 100 ppm-h treatment .