PeerJ Preprints: Ecosystem Sciencehttps://peerj.com/preprints/index.atom?journal=peerj&subject=1200Ecosystem Science articles published in PeerJ PreprintsIsolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalayahttps://peerj.com/preprints/273912019-12-212019-12-21Basharat HamidArshid JehangirZahoor Ahmad BabaMuneer Ahmad WaniImran Khan
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.Physical habitat modeling methodology and applicationshttps://peerj.com/preprints/280052019-10-032019-10-03Ravi Nalamothu
The water management districts in Florida are required by s. 373.042, F.S. to establish minimum flow and levels (MFLs) for a priority list of water bodies that is updated each year. These MFLs are established for water bodies to prevent “significant harm” to the water resources or ecology because of withdrawals for beneficial use, and can be an effective water resource management tool. Protection of the resource from significant harm is a benefit to the variety of existing users of the resource as well as the ecological systems supported by the water bodies. This article presents an overview of a modeling technique and an associated tool developed to protect the instream habitat from significant harm.
The water management districts in Florida are required by s. 373.042, F.S. to establish minimum flow and levels (MFLs) for a priority list of water bodies that is updated each year. These MFLs are established for water bodies to prevent “significant harm” to the water resources or ecology because of withdrawals for beneficial use, and can be an effective water resource management tool. Protection of the resource from significant harm is a benefit to the variety of existing users of the resource as well as the ecological systems supported by the water bodies. This article presents an overview of a modeling technique and an associated tool developed to protect the instream habitat from significant harm.Biogeographic patterns of belemnite body size responses to episodes of environmental crisishttps://peerj.com/preprints/280002019-09-302019-09-30Patrícia RitaJosé C. García-RamosPascal NeigeLaura PiñuelaRobert WeisLuís V. DuarteChristof ÜbelackerKenneth De Baets
Body size changes have been investigated through episodes of environmental crisis among several groups of organisms but the relative contribution of within-lineage size changes, selective extinction and origination of taxa on these patterns is still being debated. Rapid warming, anoxia, and perturbations of the carbon cycle linked with volcanic activity, as well as their impact on marine diversity are well documented for the Pliensbachian-Toarcian (Pli-Toa) boundary and for the Toarcian Oceanic Anoxic Event (T-OAE). Belemnites were a very abundant and successful cephalopod group in the Mesozoic oceans playing a paramount role in the oceanic trophic webs. Belemnites have mainly been studied from a geochemical perspective during this interval. Newly collected data from three northern and western Iberian sections (Peniche, Rodiles and Lastres) allowed an analysis of the belemnite body size dynamics across the Pli-Toa boundary and the T-OAE and a comparison with other European basins. In Peniche (Lusitanian Basin, Portugal), a significant reduction in belemnite body size was recognized across the Pli-Toa boundary at the assemblage level (i.e. community scale of organization). From the analysis of the different taxa recorded, it seems that adult specimens of Pseudohastites longiformis are driving the body size pattern observed (13% rostrum size decrease). The uppermost Polymorphum-Levisoni zones interval is characterized by a dramatic decrease on both belemnite abundance and diversity. Only 4 specimens of the genus Acrocoelites were found, increasing the body size at the assemblage level. In the Asturian Basin (N Spain), on the other hand, a body size increase at the assemblage level is recognized across the Pli-Toa boundary caused by a within-lineage effect mainly related to adult specimens of Passaloteuthis and Pseudohastites genera. During the onset of the T-OAE, belemnite body size increases due to the appearance of Acrocoelites genus. To summarize, the increase in rostrum size at the assemblage level across the T-OAE is associated with the radiation of a large-sized taxon (Acrocoelites genus) and the extinction of various other species. On the other hand, across the Pli-Toa boundary, the belemnite body size changes are dominated by within-lineage mechanisms. This suggests that species might have been able to cope within the early warming phase (Pli-Ta boundary), but were more affected by the subsequent warming and anoxia during the T-OAE. Our preliminary results indicate that this pattern might also be recognized in other western European sections, such as Cleveland Basin, western Paris Basin (Normandy) and Southern Germany sections. The biotic and abiotic drivers of belemnite body size changes still need to be comprehensively analyzed.
Body size changes have been investigated through episodes of environmental crisis among several groups of organisms but the relative contribution of within-lineage size changes, selective extinction and origination of taxa on these patterns is still being debated. Rapid warming, anoxia, and perturbations of the carbon cycle linked with volcanic activity, as well as their impact on marine diversity are well documented for the Pliensbachian-Toarcian (Pli-Toa) boundary and for the Toarcian Oceanic Anoxic Event (T-OAE). Belemnites were a very abundant and successful cephalopod group in the Mesozoic oceans playing a paramount role in the oceanic trophic webs. Belemnites have mainly been studied from a geochemical perspective during this interval. Newly collected data from three northern and western Iberian sections (Peniche, Rodiles and Lastres) allowed an analysis of the belemnite body size dynamics across the Pli-Toa boundary and the T-OAE and a comparison with other European basins. In Peniche (Lusitanian Basin, Portugal), a significant reduction in belemnite body size was recognized across the Pli-Toa boundary at the assemblage level (i.e. community scale of organization). From the analysis of the different taxa recorded, it seems that adult specimens of Pseudohastites longiformis are driving the body size pattern observed (13% rostrum size decrease). The uppermost Polymorphum-Levisoni zones interval is characterized by a dramatic decrease on both belemnite abundance and diversity. Only 4 specimens of the genus Acrocoelites were found, increasing the body size at the assemblage level. In the Asturian Basin (N Spain), on the other hand, a body size increase at the assemblage level is recognized across the Pli-Toa boundary caused by a within-lineage effect mainly related to adult specimens of Passaloteuthis and Pseudohastites genera. During the onset of the T-OAE, belemnite body size increases due to the appearance of Acrocoelites genus. To summarize, the increase in rostrum size at the assemblage level across the T-OAE is associated with the radiation of a large-sized taxon (Acrocoelites genus) and the extinction of various other species. On the other hand, across the Pli-Toa boundary, the belemnite body size changes are dominated by within-lineage mechanisms. This suggests that species might have been able to cope within the early warming phase (Pli-Ta boundary), but were more affected by the subsequent warming and anoxia during the T-OAE. Our preliminary results indicate that this pattern might also be recognized in other western European sections, such as Cleveland Basin, western Paris Basin (Normandy) and Southern Germany sections. The biotic and abiotic drivers of belemnite body size changes still need to be comprehensively analyzed.Mapping ecological trends by keywords in the last 20 yearshttps://peerj.com/preprints/279942019-09-302019-09-30Lei Shi
Background. An effective bibliometric analysis based on the Science Citation Index (SCI) published by the Institute of Scientific Information (ISI) was carried out to identify the trend of ecological research between 1992 and 2016. Methods. This study emphases on the high-frequency keywords and their relationships to reveal the hotspots and developing trends of ecological research fields . Results. The result shows that the hotpots of ecology has changed a lot during the last 25 years, but some topics occupied an important position in ecological research consistently. Especially, “Biodiversity” and “Climate change” have been obtained more and more attention, so their ranks also have been changed greatly. As well as, we find that the relationship of the most frequently used keywords become more closely and complicated compared to before. Another interesting and amazing result shows that the keywords related to anthropogenic increased sharply. Finally, keywords analysis was an effective approach for mapping ecological research. We guess that anthropogenic keywords may be a potential guide for future research.
Background. An effective bibliometric analysis based on the Science Citation Index (SCI) published by the Institute of Scientific Information (ISI) was carried out to identify the trend of ecological research between 1992 and 2016. Methods. This study emphases on the high-frequency keywords and their relationships to reveal the hotspots and developing trends of ecological research fields . Results. The result shows that the hotpots of ecology has changed a lot during the last 25 years, but some topics occupied an important position in ecological research consistently. Especially, “Biodiversity” and “Climate change” have been obtained more and more attention, so their ranks also have been changed greatly. As well as, we find that the relationship of the most frequently used keywords become more closely and complicated compared to before. Another interesting and amazing result shows that the keywords related to anthropogenic increased sharply. Finally, keywords analysis was an effective approach for mapping ecological research. We guess that anthropogenic keywords may be a potential guide for future research.Revegetation pattern affecting accumulation of organic carbon and total nitrogen in reclaimed mine soilshttps://peerj.com/preprints/279362019-09-052019-09-05Ping P ZhangYan L ZhangJun C JiaYong X CuiXia WangXing C ZhangYun Q Wang
Selecting optimal revegetation patterns, i.e., patterns that are more effective for soil organic carbon (SOC) and total nitrogen (TN) accumulation is particularly important for mine land reclamation. However, there have been few evaluations of the effects of different revegetation patterns on the SOC and TN in reclaimed mine soils on the Loess Plateau, China. In this study, the SOC and TN stocks were investigated at reclaimed mine sites (RMSs), including artificially revegetated sites (ARSs) (arbors [Ar], bushes [Bu], arbor-bush mixtures [AB], and grasslands [Gr]) and a natural recovery site (NRS), as well as at undisturbed native sites (UNSs). Overall, the SOC and TN stocks in the RMSs were lower than those in the UNSs over 10–13 years after reclamation. Except for those in Ar, the SOC and TN stocks in the ARSs were significantly larger than those in the NRS. Compared with those in the NRS, the total SOC stocks in the 100 cm soil interval increased by 51.4%, 59.9%, and 109.9% for Bu, AB, and Gr, respectively, and the TN stocks increased by 33.1%, 35.1%, and 57.9%. The SOC stocks in the 0 – 100 cm soil interval decreased in the order of Gr (3.78 kg m –2) > AB (2.88 kg m–2) ≥ Bu (2.72 kg m–2), and the TN stocks exhibited a similar trend. These results suggest that grasslands were more favorable than woodlands for SOC and TN accumulation in this arid area, especially in Ar. Thus, in terms of the accumulation of SOC and TN, grassland planting is recommended as a revegetation pattern for areas with reclaimed mine soils.
Selecting optimal revegetation patterns, i.e., patterns that are more effective for soil organic carbon (SOC) and total nitrogen (TN) accumulation is particularly important for mine land reclamation. However, there have been few evaluations of the effects of different revegetation patterns on the SOC and TN in reclaimed mine soils on the Loess Plateau, China. In this study, the SOC and TN stocks were investigated at reclaimed mine sites (RMSs), including artificially revegetated sites (ARSs) (arbors [Ar], bushes [Bu], arbor-bush mixtures [AB], and grasslands [Gr]) and a natural recovery site (NRS), as well as at undisturbed native sites (UNSs).Overall, the SOC and TN stocks in the RMSs were lower than those in the UNSs over 10–13 years after reclamation. Except for those in Ar, the SOC and TN stocks in the ARSs were significantly larger than those in the NRS. Compared with those in the NRS, the total SOC stocks in the 100 cm soil interval increased by 51.4%, 59.9%, and 109.9% for Bu, AB, and Gr, respectively, and the TN stocks increased by 33.1%, 35.1%, and 57.9%. The SOC stocks in the 0 – 100 cm soil interval decreased in the order of Gr (3.78 kg m –2) > AB (2.88 kg m–2) ≥ Bu (2.72 kg m–2), and the TN stocks exhibited a similar trend. These results suggest that grasslands were more favorable than woodlands for SOC and TN accumulation in this arid area, especially in Ar. Thus, in terms of the accumulation of SOC and TN, grassland planting is recommended as a revegetation pattern for areas with reclaimed mine soils.Plant litter estimation and its correlation with sediment concentration in the Loess Plateauhttps://peerj.com/preprints/278912019-08-102019-08-10Qian LiLigang MaSuhong LiuAdilai WufuYinbo LiShengtian YangXiaodong Yang
Background. Sediment concentration in the water of the loess Plateau region has dramatically decreased during the past two decades. Plant litter is considered to be one of the most important factors for this change. Existing remote sensing studies that focus on plant litter mainly use extraction methods based on vegetation indices or changes in the plant litter. Few studies have conducted time series analyses of plant litter or considered the correlation between plant litter and soil erosion. In addition, social factors are not given enough consideration in the remote sensing and soil community. Methods. This study performs time series estimation of plant litter by integrating three-scale remotely sensed data and a random forest (RF) modeling algorithm. Predictive models are used to estimate the spatially explicit plant litter cover for the entire Loess Plateau over the last two decades (2000–2018). Then, the sediment concentration in the water was classified into 9 grades based on environmental and social-economic factors. Results. Our results demonstrate the effectiveness of the proposed predictive models at the regional scale. The areas with increased plant litter cover accounted for 67% of the total area, while the areas with decreased plant litter cover accounted for 33% of the total area. In addition, plant litter is demonstrated to be one of the top three factors contributing to the decrease in the river sediment concentration. Social-economic factors were also important for the decrease of the sediment concentration in the water, for example, the population of the rural area.
Background. Sediment concentration in the water of the loess Plateau region has dramatically decreased during the past two decades. Plant litter is considered to be one of the most important factors for this change. Existing remote sensing studies that focus on plant litter mainly use extraction methods based on vegetation indices or changes in the plant litter. Few studies have conducted time series analyses of plant litter or considered the correlation between plant litter and soil erosion. In addition, social factors are not given enough consideration in the remote sensing and soil community. Methods. This study performs time series estimation of plant litter by integrating three-scale remotely sensed data and a random forest (RF) modeling algorithm. Predictive models are used to estimate the spatially explicit plant litter cover for the entire Loess Plateau over the last two decades (2000–2018). Then, the sediment concentration in the water was classified into 9 grades based on environmental and social-economic factors. Results. Our results demonstrate the effectiveness of the proposed predictive models at the regional scale. The areas with increased plant litter cover accounted for 67% of the total area, while the areas with decreased plant litter cover accounted for 33% of the total area. In addition, plant litter is demonstrated to be one of the top three factors contributing to the decrease in the river sediment concentration. Social-economic factors were also important for the decrease of the sediment concentration in the water, for example, the population of the rural area.Below the canopy: global trends in forest vertebrate populations and their drivershttps://peerj.com/preprints/278822019-08-012019-08-01Elizabeth J. GreenLouise McRaeRobin FreemanMike B.J. HarfootSamantha L.L. HillWilliam Baldwin-CantelloWilliam D. Simonson
Global forest assessments use forest area as a proxy indicator of biodiversity status, which may mask below-canopy pressures driving forest biodiversity loss and ‘empty forest’ syndrome. The status of forest biodiversity is important not only for species conservation but also because species loss can have consequences for forest health and carbon storage. We aimed to develop a global indicator of forest specialist vertebrate populations to improve assessments of forest biodiversity status. For this purpose we used the Living Planet Index methodology, developing a weighted composite Forest Specialist Index for the period 1970-2014. We then investigated potential drivers of forest vertebrate population change, including tree cover change, to determine whether forest area is a good proxy for forest biodiversity. The effects of satellite-derived tree cover trends and other pressures on the average rate of change of forest vertebrate populations were analysed. We reviewed the literature to gain more context-specific information relating to drivers of forest specialist population change. On average, forest vertebrate populations declined by 53% between 1970 and 2014. We found little evidence of a consistent global effect of tree cover change on forest vertebrate populations but a significant negative effect of exploitation threat on forest specialists. However, time-series cross-correlation analyses showed some forest specialist populations are closely aligned to tree cover change. The literature review identified several drivers of population change that cannot be detected remotely and may cause populations to change independently of tree cover. Forest vertebrate populations have more than halved since the 1970s. In conclusion, we found that forest area is a poor proxy of forest biodiversity status. For forest biodiversity to recover, we must monitor and manage all threats to vertebrates, including those below the canopy.
Global forest assessments use forest area as a proxy indicator of biodiversity status, which may mask below-canopy pressures driving forest biodiversity loss and ‘empty forest’ syndrome. The status of forest biodiversity is important not only for species conservation but also because species loss can have consequences for forest health and carbon storage. We aimed to develop a global indicator of forest specialist vertebrate populations to improve assessments of forest biodiversity status. For this purpose we used the Living Planet Index methodology, developing a weighted composite Forest Specialist Index for the period 1970-2014. We then investigated potential drivers of forest vertebrate population change, including tree cover change, to determine whether forest area is a good proxy for forest biodiversity. The effects of satellite-derived tree cover trends and other pressures on the average rate of change of forest vertebrate populations were analysed. We reviewed the literature to gain more context-specific information relating to drivers of forest specialist population change. On average, forest vertebrate populations declined by 53% between 1970 and 2014. We found little evidence of a consistent global effect of tree cover change on forest vertebrate populations but a significant negative effect of exploitation threat on forest specialists. However, time-series cross-correlation analyses showed some forest specialist populations are closely aligned to tree cover change. The literature review identified several drivers of population change that cannot be detected remotely and may cause populations to change independently of tree cover. Forest vertebrate populations have more than halved since the 1970s. In conclusion, we found that forest area is a poor proxy of forest biodiversity status. For forest biodiversity to recover, we must monitor and manage all threats to vertebrates, including those below the canopy.Failure to respond to a coral disease outbreak: Potential costs and consequenceshttps://peerj.com/preprints/278602019-07-162019-07-16William F Precht
A coral disease with white plague-like signs was observed near Virginia Key, Florida, in September 2014. The disease outbreak directly followed a regional high temperature coral-bleaching event. Now called stony coral tissue loss disease (SCTLD), it has spread the length of the Florida Reef Tract from Key West to Martin County, a distance of about 450 km. Recently, the disease has also been observed at a number of sites throughout the Caribbean. The high prevalence of disease, the number of susceptible species, and the high mortality of corals affected suggests this outbreak is arguably one of the most lethal ever recorded. The initial response to this catastrophic disease by resource mangers with purview over the ecosystem was slow. There is generally a very short window of opportunity to intervene in disease amelioration or eradication in the marine environment. This slow response enabled the disease to spread unchecked. Why was the response to the loss of our coral reefs to a coral disease epidemic, such a massive failure? This includes our failure as scientists, regulators, resource managers, the local media, and policy makers alike. This review encapsulates the numerous reasons for our failures during the first few years of the outbreak. Specifically, I show how the Port Miami dredging project that was ongoing at the time of the initial outbreak created a distraction as local NGO's, regulatory agencies, and resource managers initially blamed the project for observed large-scale coral losses. However, detailed analysis of 650 tagged corals that were part of a repeated measures monitoring program required for permit compliance associated with the Port Miami dredge project reveal that both disease susceptibility and coral mortality are invariant with the results collected by a number of scientific teams throughout the region. Finally, when the agencies responded to the outbreak the effort it was too little and much too late to make a meaningful difference. Because of the languid management response to this outbreak, we are now sadly faced with a situation where much of our management efforts are focused on the rescue of genetic material from coral species now at risk of regional extinction.
A coral disease with white plague-like signs was observed near Virginia Key, Florida, in September 2014. The disease outbreak directly followed a regional high temperature coral-bleaching event. Now called stony coral tissue loss disease (SCTLD), it has spread the length of the Florida Reef Tract from Key West to Martin County, a distance of about 450 km. Recently, the disease has also been observed at a number of sites throughout the Caribbean. The high prevalence of disease, the number of susceptible species, and the high mortality of corals affected suggests this outbreak is arguably one of the most lethal ever recorded. The initial response to this catastrophic disease by resource mangers with purview over the ecosystem was slow. There is generally a very short window of opportunity to intervene in disease amelioration or eradication in the marine environment. This slow response enabled the disease to spread unchecked. Why was the response to the loss of our coral reefs to a coral disease epidemic, such a massive failure? This includes our failure as scientists, regulators, resource managers, the local media, and policy makers alike. This review encapsulates the numerous reasons for our failures during the first few years of the outbreak. Specifically, I show how the Port Miami dredging project that was ongoing at the time of the initial outbreak created a distraction as local NGO's, regulatory agencies, and resource managers initially blamed the project for observed large-scale coral losses. However, detailed analysis of 650 tagged corals that were part of a repeated measures monitoring program required for permit compliance associated with the Port Miami dredge project reveal that both disease susceptibility and coral mortality are invariant with the results collected by a number of scientific teams throughout the region. Finally, when the agencies responded to the outbreak the effort it was too little and much too late to make a meaningful difference. Because of the languid management response to this outbreak, we are now sadly faced with a situation where much of our management efforts are focused on the rescue of genetic material from coral species now at risk of regional extinction.Validation of COI metabarcoding primers for terrestrial arthropodshttps://peerj.com/preprints/278012019-07-152019-07-15Vasco ElbrechtThomas WA BraukmannNatalia V IvanovaSean WJ ProsserMehrdad HajibabaeiMichael WrightEvgeny V ZakharovPaul DN HebertDirk Steinke
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. Thus this study tests the performance of 36 primer sets on a mock community containing 374 species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets where also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from the 21 amplicon pools of the mock community and Malaise trap sample were used to select four primer sets for metabarcoding evaluation at different annealing temperatures (40-60 Co) using the mock community. Temperature did only have a minor effect on taxa recovery that varied with the specific primer pair. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrated that certain primer sets can recover most taxa in a diverse species assemblage. Thus there is no need to employ several primer sets targeting the same amplicon. While we identified several suited primer sets for arthropod metabarcoding, the primer selection depends on the targeted taxonomic groups, as well as DNA quality, desired taxonomic resolution, and sequencing platform employed for analysis.
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. Thus this study tests the performance of 36 primer sets on a mock community containing 374 species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets where also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from the 21 amplicon pools of the mock community and Malaise trap sample were used to select four primer sets for metabarcoding evaluation at different annealing temperatures (40-60 Co) using the mock community. Temperature did only have a minor effect on taxa recovery that varied with the specific primer pair. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrated that certain primer sets can recover most taxa in a diverse species assemblage. Thus there is no need to employ several primer sets targeting the same amplicon. While we identified several suited primer sets for arthropod metabarcoding, the primer selection depends on the targeted taxonomic groups, as well as DNA quality, desired taxonomic resolution, and sequencing platform employed for analysis.A new primer for metabarcoding of spider gut contentshttps://peerj.com/preprints/278542019-07-122019-07-12Denis LafageVasco ElbrechtJordan CuffDirk SteinkePeter HambäckAnn Erlandsson
As a key predator group, spiders have received a lot of attention by food web ecologists in diverse fields such as pest control, pollutant transfers, and cross-ecosystem fluxes. The difficulty involved in studying their diet has led to the use of new technologies such as metabarcoding of gut contents. The amplification of a broad range of spider prey without amplifying spiders themselves is challenging and, until now, an efficient universal primer purposed for this has not existed.
We developed a novel forward primer (NoSpi2) targeting the cytochrome c oxidase subunit I gene. The primer was designed not to amplify spiders of the oval calamistrum clade (Lycosidae and closely related species) while still amplifying most other invertebrates. NoSpi2 was tested together with the reverse primer BR2 in silico, in vitro on single specimens of prey and spiders, on mock and malaise trap communities, and in an ecological application.
In silico evaluation predicted high primer bias for spiders of the oval calamistrum clade and low bias for all other invertebrates. These results were largely confirmed by in vitro tests. Additionally, some spider families were not amplified contrary to our expectations. We demonstrated a high efficiency for the primer pair NoSpi2/BR2 which recovered up to 94% of taxa in the mock community and 85% of the taxa detected by the best invertebrate primer pair known (BF3+BR2) for the malaise trap community. The field experiment showed that Lycosidae spider DNA is not amplified by the NoSpi2 primer set. It also demonstrated a broad range of detectable prey species. We found prey from 12 orders, 67 families and 117 species.
The ability of the NoSpi2/BR2 primer combination to reliably amplify prey species, without amplifying any predator reads, makes it an ideal choice for gut-content analysis for spider species of lycosids and closely related species, even enabling the homogenization of entire spider specimens without dissection. Given that the detected prey species included other spiders and carabid beetles, this primer could be used for not only diet and biological control studies, but also to study intra-guild predation.
As a key predator group, spiders have received a lot of attention by food web ecologists in diverse fields such as pest control, pollutant transfers, and cross-ecosystem fluxes. The difficulty involved in studying their diet has led to the use of new technologies such as metabarcoding of gut contents. The amplification of a broad range of spider prey without amplifying spiders themselves is challenging and, until now, an efficient universal primer purposed for this has not existed.We developed a novel forward primer (NoSpi2) targeting the cytochrome c oxidase subunit I gene. The primer was designed not to amplify spiders of the oval calamistrum clade (Lycosidae and closely related species) while still amplifying most other invertebrates. NoSpi2 was tested together with the reverse primer BR2 in silico, in vitro on single specimens of prey and spiders, on mock and malaise trap communities, and in an ecological application.In silico evaluation predicted high primer bias for spiders of the oval calamistrum clade and low bias for all other invertebrates. These results were largely confirmed by in vitro tests. Additionally, some spider families were not amplified contrary to our expectations. We demonstrated a high efficiency for the primer pair NoSpi2/BR2 which recovered up to 94% of taxa in the mock community and 85% of the taxa detected by the best invertebrate primer pair known (BF3+BR2) for the malaise trap community. The field experiment showed that Lycosidae spider DNA is not amplified by the NoSpi2 primer set. It also demonstrated a broad range of detectable prey species. We found prey from 12 orders, 67 families and 117 species.The ability of the NoSpi2/BR2 primer combination to reliably amplify prey species, without amplifying any predator reads, makes it an ideal choice for gut-content analysis for spider species of lycosids and closely related species, even enabling the homogenization of entire spider specimens without dissection. Given that the detected prey species included other spiders and carabid beetles, this primer could be used for not only diet and biological control studies, but also to study intra-guild predation.