scholarly journals Identifying the potential of anadromous salmonid habitat restoration with life cycle models

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256792
Author(s):  
Jeffrey C. Jorgensen ◽  
Colin Nicol ◽  
Caleb Fogel ◽  
Timothy J. Beechie
Keyword(s):  
Life Cycle ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Coho Salmon ◽  
Life Stage ◽  
Fine Sediment ◽  
Life Stages ◽  
Beaver Pond ◽  
Barrier Removal ◽  
Life Cycle Models

An investigation into the causes of species decline should include examination of habitats important for multiple life stages. Integrating habitat impacts across life stages with life-cycle models (LCMs) can reveal habitat impairments inhibiting recovery and help guide restoration efforts. As part of the final elements of the Habitat Restoration Planning model (HARP; Beechie et al. this volume), we developed LCMs for four populations of three species of anadromous salmonids (Oncorhynchus kisutch, O. tshawytscha, and O. mykiss), and ran diagnostic scenarios to examine effects of barrier removal, fine sediment reduction, wood augmentation, riparian shade, restoration of the main channel and bank conditions, beaver pond restoration, and floodplain reconnection. In the wood scenario, spawner abundance for all populations increased moderately (29–48%). In the shade scenario, spring-run Chinook salmon abundance increased the most (48%) and fall-run Chinook salmon and steelhead were much less responsive. Coho responded strongly to the beaver pond and floodplain scenarios (76% and 54%, respectively). The fine sediment scenario most benefitted fall- and spring-run Chinook salmon (32–63%), whereas steelhead and coho were less responsive (11–21% increase). More observations are needed to understand high fine sediment and its impacts. Our LCMs were region-specific, identifying places where habitat actions had the highest potential effects. For example, the increase in spring-run Chinook salmon in the wood scenario was driven by the Cascade Mountains Ecological Region. And, although the overall response of coho salmon was small in the barrier removal scenario (6% increase at the scale of the entire basin), barrier removals had important sub-regional impacts. The HARP analysis revealed basin-wide and regional population-specific potential benefits by action types, and this habitat-based approach could be used to develop restoration strategies and guide population rebuilding. An important next step will be to ground-truth our findings with robust empirically-based estimates of life stage-specific survivals and abundances.

scholarly journals Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei

2021 ◽  
Vol 12 ◽  
Author(s):  
Fernan Santiago Mejía-Alvarado ◽  
Thaura Ghneim-Herrera ◽  
Carmenza E. Góngora ◽  
Pablo Benavides ◽  
Lucio Navarro-Escalante
Keyword(s):  
Life Cycle ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Developmental Stages ◽  
Life Stage ◽  
Insect Control ◽  
Life Stages ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Structure And Dynamics

The coffee berry borer (CBB); Hypothenemus hampei (Coleoptera: Curculionidae), is widely recognized as the major insect pest of coffee crops. Like many other arthropods, CBB harbors numerous bacteria species that may have important physiological roles in host nutrition, detoxification, immunity and protection. To date, the structure and dynamics of the gut-associated bacterial community across the CBB life cycle is not yet well understood. A better understanding of the complex relationship between CBB and its bacterial companions may provide new opportunities for insect control. In the current investigation, we analyzed the diversity and abundance of gut microbiota across the CBB developmental stages under field conditions by using high-throughput Illumina sequencing of the 16S ribosomal RNA gene. Overall, 15 bacterial phyla, 38 classes, 61 orders, 101 families and 177 genera were identified across all life stages, including egg, larva 1, larva 2, pupa, and adults (female and male). Proteobacteria and Firmicutes phyla dominated the microbiota along the entire insect life cycle. Among the 177 genera, the 10 most abundant were members of Ochrobactrum (15.1%), Pantoea (6.6%), Erwinia (5.7%), Lactobacillus (4.3%), Acinetobacter (3.4%), Stenotrophomonas (3.1%), Akkermansia (3.0%), Agrobacterium (2.9%), Curtobacterium (2.7%), and Clostridium (2.7%). We found that the overall bacterial composition is diverse, variable within each life stage and appears to vary across development. About 20% of the identified OTUs were shared across all life stages, from which 28 OTUs were consistently found in all life stage replicates. Among these OTUs there are members of genera Pantoea, Erwinia, Agrobacterium, Ochrobactrum, Pseudomonas, Acinetobacter, Brachybacterium, Sphingomonas and Methylobacterium, which can be considered as the gut-associated core microbiota of H. hampei. Our findings bring additional data to enrich the understanding of gut microbiota in CBB and its possible use for development of insect control strategies.

A Bayesian life-cycle model to estimate escapement at maximum sustained yield in salmon based on limited information

2019 ◽  
Vol 76 (2) ◽  
pp. 299-307
Author(s):  
Jan Ohlberger ◽  
Samuel J. Brenkman ◽  
Patrick Crain ◽  
George R. Pess ◽  
Jeffrey J. Duda ◽  
...  
Keyword(s):  
Life Cycle ◽  
Time Series Data ◽  
Coho Salmon ◽  
Reference Points ◽  
Series Data ◽  
Limited Information ◽  
Maximum Sustained Yield ◽  
Sustained Yield ◽  
Life Cycle Models ◽  
Marine Survival

Life-cycle models combine several strengths for estimating population parameters and biological reference points of harvested species and are particularly useful for those exhibiting distinct habitat shifts and experiencing contrasting environments. Unfortunately, time series data are often limited to counts of adult abundance and harvest. By incorporating data from other populations and by dynamically linking the life-history stages, Bayesian life-cycle models can be used to estimate stage-specific productivities and capacities as well as abundance of breeders that produce maximum sustained yield (MSY). Using coho salmon (Oncorhynchus kisutch) as our case study, we show that incorporating information on marine survival variability from nearby populations can improve model estimates and affect management parameters such as escapement at MSY. We further show that the expected long-term average yield of a fishery managed for a spawner escapement target that produces MSY strongly depends on the average marine survival. Our results illustrate the usefulness of incorporating information from other sources and highlight the importance of accounting for variation in marine survival when making inferences about the management of Pacific salmon.

scholarly journals Predicting the effects of climate change on freshwater cyanobacterial blooms requires consideration of the complete cyanobacterial life cycle

2020 ◽  
Author(s):  
Kathryn L Cottingham ◽  
Kathleen C Weathers ◽  
Holly A Ewing ◽  
Meredith L Greer ◽  
Cayelan C Carey
Keyword(s):  
Climate Change ◽  
Life Cycle ◽  
Climate Models ◽  
Empirical Studies ◽  
Life Stage ◽  
Cyanobacterial Blooms ◽  
Life Stages ◽  
Ecosystem Models ◽  
Complete Life Cycle ◽  
Integrated Research

Abstract To date, most research on cyanobacterial blooms in freshwater lakes has focused on the pelagic life stage. However, examining the complete cyanobacterial life cycle—including benthic life stages—may be needed to accurately predict future bloom dynamics. The current expectation, derived from the pelagic life stage, is that blooms will continue to increase due to the warmer temperatures and stronger stratification associated with climate change. However, stratification and mixing have contrasting effects on different life stages: while pelagic cyanobacteria benefit from strong stratification and are adversely affected by mixing, benthic stages can benefit from increased mixing. The net effects of these potentially counteracting processes are not yet known, since most aquatic ecosystem models do not incorporate benthic stages and few empirical studies have tracked the complete life cycle over multiple years. Moreover, for many regions, climate models project both stronger stratification and increased storm-induced mixing in the coming decades; the net effects of those physical processes, even on the pelagic life stage, are not yet understood. We therefore recommend an integrated research agenda to study the dual effects of stratification and mixing on the complete cyanobacterial life cycle—both benthic and pelagic stages—using models, field observations and experiments.

Pacific Salmon: Ecology and Management of Western Alaska’s Populations

2009 ◽  
Keyword(s):  
Chinook Salmon ◽  
Chum Salmon ◽  
Coho Salmon ◽  
Life Stage ◽  
Early Summer ◽  
Juvenile Salmon ◽  
Ice Melt ◽  
Estuarine Ecology ◽  
Species Abundances ◽  
Salinity Water

<em>Abstract.</em>—In the late 1990s and early 2000s, large declines in numbers of chum salmon <em>Oncorhynchus keta </em>and Chinook salmon <em>O. tshawytscha </em>returning to the Arctic-Yukon-Kuskokwim (AYK) region (Alaska, USA) illuminated the need for an improved understanding of the variables controlling salmon abundance at all life stages. In addressing questions about salmon abundance, large gaps in our knowledge of basic salmon life history and the critical early marine life stage were revealed. In this paper, results from studies conducted on the estuarine ecology of juvenile salmon in western Alaska are summarized and compared, emphasizing timing and distribution during outmigration, environmental conditions, age and growth, feeding, and energy content of salmon smolts. In western Alaska, water temperature dramatically changes with season, ranging from 0°C after ice melt in late spring/early summer to 19°C in July. Juvenile salmon were found in AYK estuaries from early May until August or September, but to date no information is available on their residence duration or survival probability. Chum salmon were the most abundant juvenile salmon reported, ranging in percent catch from <0.1% to 4.7% and most research effort has focused on this species. Abundances of Chinook salmon, sockeye salmon <em>O. nerka</em>, and pink salmon <em>O. gorbuscha </em>varied among estuaries, while coho salmon <em>O. kisutch </em>juveniles were consistently rare, never amounting to more than 0.8% of the catch. Dietary composition of juvenile salmon was highly variable and a shift was commonly reported from epibenthic and neustonic prey in lower salinity water to pelagic prey in higher salinity water. Gaps in the knowledge of AYK salmon estuarine ecology are still evident. For example, data on outmigration patterns and residence timing and duration, rearing conditions and their effect on diet, growth, and survival are often completely lacking or available only for few selected years and sites. Filling gaps in knowledge concerning salmon use and survival in estuarine and near-shore habitats within the AYK region will aid in assessing the relative roles of all habitats (freshwater to marine) in controlling salmon abundance.

scholarly journals Can the creation of new freshwater habitat demographically offset losses of Pacific salmon from chronic anthropogenic mortality?

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0237052
Author(s):  
Pascale Gibeau ◽  
Michael J. Bradford ◽  
Wendy J. Palen
Keyword(s):  
Pacific Northwest ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Life Stage ◽  
Life Stages ◽  
Typical Size ◽  
Side Channels ◽  
Lower Productivity ◽  
Freshwater Habitats ◽  
The Creation

Over 1 billion USD are devoted annually to rehabilitating freshwater habitats to improve survival for the recovery of endangered salmon populations. Mitigation often requires the creation of new habitat (e.g. habitat offsetting) to compensate population losses from human activities, however offsetting schemes are rarely evaluated. Anadromous Pacific salmon are ecologically, culturally, and economically important in the US and Canada, and face numerous threats from degradation of freshwater habitats. Here we used a matrix population model of coho salmon (Oncorhynchus kisutch) to determine the amount of habitat offsetting needed to compensate mortality (2–20% per year) caused by a range of development activities. We simulated chronic mortality to three different life stages (egg, parr, smolt/adult), individually and simultaneously, to mimic impacts from development, and evaluated if the number of smolts produced from constructed side-channels demographically offset losses. We show that under ideal conditions, the typical size of a constructed side-channel in the Pacific Northwest (PNW) (3405 m2) is sufficient to compensate for only relatively low levels of chronic mortality to either the parr or smolt/adult stages (2–7% per year), but populations do not recover if mortality is >10% per year. When we assumed lower productivity (e.g.; 25th percentile), we found that constructed channels would need to be 2.5–4.5 fold larger as compared to the typical size built in the PNW, respectively, to maintain population sizes. Moreover, when we imposed mortality to parr and smolt/adult stages simultaneously, we found that constructed side-channels would need to be between 1.8- and 2.3- fold larger that if the extra chronic mortality was imposed to one life stage only. We conclude that habitat offsetting has the potential to mitigate chronic mortality to early life stages, but that realistic assumptions about productivity of constructed side-channels and cumulative effects of anthropogenic disturbances on multiple life stages need to be considered.

Predator avoidance in naive and experienced juvenile chinook and coho salmon

1995 ◽  
Vol 52 (3) ◽  
pp. 614-622 ◽  
Author(s):  
M. C. Healey ◽  
U. Reinhardt
Keyword(s):  
Open Field ◽  
Risk Taking ◽  
Chinook Salmon ◽  
Predator Avoidance ◽  
Coho Salmon ◽  
Capture Rate ◽  
Risk Exposure ◽  
Life Stages ◽  
Specific Behaviour ◽  
Species Specific

We compared the vulnerability of naive and experienced coho and chinook salmon to predation by rainbow trout and related these findings to observations of the specific behaviour of each species during an encounter with the predator. Naive chinook were significantly less vulnerable to capture than naive coho in an open field encounter but there was no difference in capture rate of experienced coho and chinook. In videotaped encounters we found that coho and chinook behaved in significantly different ways when attacked by the predator, both when naive and when experienced. Our results suggest that predator avoidance strategies are highly species specific, that both species adjusted their behaviour after experience with the predator, and that the behavioural changes adopted by coho improved their ability to avoid the predator in an open field but those adopted by chinook did not. Considerable recent research has explored the willingness of different species, sexes, or life stages to risk exposure to a predator to obtain some reward (usually food). Our results further suggest that published experiments that purport to demonstrate differences in risk taking among types of prey may, instead, demonstrate differences in predator avoidance capability.

Do chemically contaminated river estuaries in Puget Sound (Washington, USA) affect the survival rate of hatchery-reared Chinook salmon?

2014 ◽  
Vol 71 (1) ◽  
pp. 162-180 ◽  
Author(s):  
James P. Meador
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Coho Salmon ◽  
Life Stage ◽  
Puget Sound ◽  
Adult Life ◽  
Parallel Analysis ◽  
Differential Survival ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

This study examined the rate of survival for hatchery-reared, ocean-type juvenile Chinook salmon (Oncorhynchus tshawytscha) to the adult life stage in relation to contamination status for estuaries where they temporarily reside. The hypothesis tested here is that juvenile Chinook from Puget Sound (Washington, USA) area hatcheries exhibit differential survival as categorized by the state of contamination in their respective natal estuaries. Data were examined from 20 hatcheries that released fish to 14 local estuaries in the Greater Puget Sound area over 37 years (1972–2008). A parallel analysis was also conducted for coho salmon (Oncorhynchus kisutch) outmigrating from many of the same hatcheries. For all years combined, juvenile Chinook transiting contaminated estuaries exhibited an overall rate of survival that was 45% lower than that for Chinook moving through uncontaminated estuaries, which was confirmed when tested year by year. The results for coho originating from the same hatcheries and sharing a similar marine distribution indicated no substantial differences among estuaries. These observations have important implications for wild juvenile Chinook that spend more time in the estuary compared with hatchery-reared fish.

Interannual variability in life-stage specific survival and life history diversity of coho salmon in a coastal Oregon basin

2021 ◽  
Author(s):  
Kim K Jones ◽  
Trevan J Cornwell ◽  
Daniel L. Bottom ◽  
Staci Stein ◽  
Steven Starcevich
Keyword(s):  
Population Dynamics ◽  
Life History ◽  
Life Cycle ◽  
Interannual Variability ◽  
Coho Salmon ◽  
Life Stage ◽  
Full Range ◽  
Life Cycle Approach ◽  
Surplus Production ◽  
Life History Patterns

We quantified the population dynamics and life history diversity of seven brood years of coho salmon using a life-cycle approach. Four life history patterns, composed of fry, fry–nomad, parr, and yearling migrants indicated the importance of connectivity and access to a full range of freshwater and estuarine rearing environments through the year. Survival of each life history type varied annually with the yearling migrants contributing an average of 70% to the spawners in all but one return year. Fifty eight percent of the spawners of the 2013 return year had an estuarine rearing strategy, primarily parr migrants that overwintered in the estuary. Fry migrants, thought to be surplus production, were consistently observed in the estuary and represented in the returning spawners. The annual contribution of alternative rearing strategies to the spawners may support the resilience and viability of the population. We recommend that life cycle models of coho salmon account for the contribution of estuary migrants to the productivity and persistence of coho salmon in support of management and restoration of populations.

scholarly journals Life Cycle Effects on the Vertical Structure of Precipitation in East China Measured by Himawari-8 and GPM DPR

2018 ◽  
Vol 146 (7) ◽  
pp. 2183-2199 ◽  
Author(s):  
Aoqi Zhang ◽  
Yunfei Fu
Keyword(s):  
Life Cycle ◽  
Brightness Temperature ◽  
Vertical Structure ◽  
Life Stage ◽  
Life Cycle Stage ◽  
Precipitation Event ◽  
Mature Stage ◽  
Life Stages ◽  
Dual Frequency ◽  
Cloud Water Content

Abstract We identified precipitating systems from May to August 2016 using data from the Global Precipitation Measurement mission Dual-frequency Precipitation Radar instrument. Then, using this set of cases, Himawari-8 10.4-μm brightness temperature data from before and after each precipitation event were used to identify three life stages of clouds: a developing stage, a mature stage, and a dissipating stage. Using statistical analysis and two case studies, we show that the precipitating systems at different life stages of the clouds have different systematic properties, including the area of precipitation, the convective ratio, the rain-top height, and the brightness temperature. The developing systems had the largest convective ratio, whereas the dissipating systems had the largest area of precipitation. The life stage of the cloud also influenced the vertical structure of the precipitation. The microphysical processes within each stage were unique, leading to various properties of the droplets in precipitation. The developing systems had large, but sparse, droplets; the mature systems had large and dense droplets; and the dissipating systems had small and sparse droplets. Our results suggest that the different properties of precipitating systems in each life cycle stage of clouds are linked to the cloud water content and the upward motion of air.

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