Carbon accumulation and vertical accretion in a restored versus historic salt marsh in southern Puget Sound,Washington, United States

Few comparisons exist between vertical accretion (VA) and carbon accumulation rates (CARs) in restored versus historic (i.e. reference) marshes. Here, we compare these processes in a formerly diked, sparsely vegetated, restored salt marsh (Six Gill Slough, SG), whose surface is subsided relative to the tidal frame, to an adjacent, relatively pristine, historic salt marsh (Animal Slough, AS). Six sediment cores were collected at both AS and SG approximately 6 years after restoration. Cores were analyzed for bulk density (BD), % loss of ignition, % organic carbon, and ²¹⁰Pb. We found that sharp changes in BD in surface layers of SG cores were highly reliable markers for the onset of restoration. The mean VA since restoration at SG (0.79 [SD = 0.29] cm/year) was approximately twice that of AS (0.41 [SD = 0.16] cm/year). In comparison, the VA at AS over 50 years was 0.30 (SD = 0.09) cm/year. VA consisted almost entirely of inorganic sediment at SG whereas at AS it was approximately 55%. Mean CARs at SG were somewhat greater than at AS, but the difference was not significant due to high variability (SG: 81–210 g C m^?2 year^?1; AS: 115–168 g C m^?2 year^?1). The mean CAR at AS over the past 50 years was 118 (SD = 23) g C m^?2 year^?1. This study demonstrates that a sparsely vegetated, restored salt marsh can quickly begin to accumulate carbon and that historic and restored marshes can have similar CARs despite highly divergent formation processes.     

In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry

Affinity purification coupled to mass spectrometry provides a reliable method for identifying proteins and their binding partners. In this study we have used Drosophila melanogaster proteins triple tagged with Flag, Strep II, and Yellow fluorescent protein in vivo within affinity pull-down experiments and isolated these proteins in their native complexes from embryos. We describe a pipeline for determining interactomes by Parallel Affinity Capture (iPAC) and show its use by identifying partners of several protein baits with a range of sizes and subcellular locations. This purification protocol employs the different tags in parallel and involves detailed comparison of resulting mass spectrometry data sets, ensuring the interaction lists achieved are of high confidence. We show that this approach identifies known interactors of bait proteins as well as novel interaction partners by comparing data achieved with published interaction data sets. The high confidence in vivo protein data sets presented here add new data to the currently incomplete D. melanogaster interactome. Additionally we report contaminant proteins that are persistent with affinity purifications irrespective of the tagged bait.     

A New Hybrid Rescue Allele in Drosophila melanogaster

Crosses of Drosophila melanogaster females to males of its sibling species Drosophila simulans, Drosophila mauritiana and Drosophila sechellia produce no sons and daughters that are viable only at low temperatures. We describe here a novel rescue allele Df(1)EP307-1-2 isolated on the basis of its suppression of high temperature hybrid female lethality. Df(1)EP307-1-2 also rescues hybrid males to the pharate adult stage, the same stage at which it is lethal to D. melanogaster pure species males. Molecular analysis indicates that Df(1)EP307-1-2 is associated with a deletion of about 61 kb in the 9D region of the X chromosome. The structure of Df(1)EP307-1-2 suggests that it was formed by a process similar to P-element induced male recombination.     

Gauging resource exploitation by juvenile Chinook salmon (Oncorhynchus tshawytscha) in restoring estuarine habitat

In the context of delta restoration and its impact on salmonid rearing, success is best evaluated based on whether out‐migrating juvenile salmon can access and benefit from suitable estuarine habitat. Here, we integrated 3 years of post‐restoration monitoring data including habitat availability, invertebrate prey biomass, and juvenile Chinook salmon (Oncorhynchus tshawytscha) physiological condition to determine whether individuals profited from the addition of 364 ha of delta habitat in South Puget Sound, Washington, United States. Productivity in the restored mudflat was comparable to reference sites 3 years after dike removal, surpassing a mean total of 6 million kJ energy from invertebrate prey. This resulted from the development of a complex network of tidal channels and a resurgence in dipteran biomass that was unique to the restoration area. Consequently, a notable shift in invertebrate consumption occurred between 2010 and 2011, whereby individuals switched from eating primarily amphipods to dipteran flies; however, dietary similarity to the surrounding habitat did not change from year to year, suggesting that this shift was a result of a change in the surrounding prey communities. Growth rates did not differ between restored and reference sites, but catch weight was positively correlated with prey biomass, where greater prey productivity appeared to offset potential density‐dependent effects. These results demonstrate how the realized function of restoring estuarine habitat is functionally dependent. High prey productivity in areas with greater connectivity may support healthy juvenile salmon that are more likely to reach the critical size class for offshore survival.     

The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster

We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p[RS3] and p[RS5], to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate >12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence.     

Changes in habitat availability for outmigrating juvenile salmon (Oncorhynchus spp.) following estuary restoration

The restoration of the Nisqually River Delta (Washington, U.S.A.) represents one of the largest efforts toward reestablishing the ecosystem function and resilience of modified habitat in the Puget Sound, particularly for anadromous salmonid species. The opportunity for outmigrating salmon to access and benefit from the expansion of available tidal habitat can be quantified by several physical attributes, which are related to the ecological and physiological responses of juvenile salmon. We monitored a variety of physical parameters to measure changes in opportunity potential from historic, pre‐restoration, and post‐restoration habitat conditions at several sites across the delta. These parameters included channel morphology, water quality, tidal elevation, and landscape connectivity. We conducted fish catch surveys across the delta to determine if salmon was utilizing restored estuary habitat. Overall major channel area increased 42% and major channel length increased 131% from pre‐ to post‐restoration conditions. Furthermore, the results of our tidal inundation model indicated that major channels were accessible up to 75% of the time, as opposed to 30% pre‐restoration. Outmigrating salmon utilized this newly accessible habitat as quickly as 1 year post‐restoration. The presence of salmon in restored tidal channels confirmed rapid post‐restoration increases in opportunity potential on the delta despite habitat quality differences between restored and reference sites.     

Beavers (Castor canadensis) facilitate early access by Canada geese (Branta canadensis) to nesting habitat and areas of open water in Canada's boreal wetlands

Several studies demonstrate how beavers influence waterfowl habitat availability, ultimately improving waterfowl breeding success; however, no current research links beavers to early season nesting activities of Canada geese (Branta canadensis) in northern climates. We examined how beavers facilitate early access to open water for geese at Miquelon Lake Provincial Park (MLPP), Canada. We surveyed 32 active and 39 inactive beaver ponds to examine whether beavers facilitate early access to open water. Open water occurred 10.7 days earlier at active beaver ponds (mean ice-off day = 87.54, s = 13.88) than inactive ponds (mean ice-off day = 98.19, s = 9.07), especially adjacent to main lodge entrances and winter food caches. Snowpack was on average 5.9 cm shallower at active ponds. Prior to availability of open water, Canada geese exhibited intraspecific territoriality over beaver lodges as nest sites and once water was present, preferred island lodges over bank lodges. These findings support other studies that examined island nesting as protection from terrestrial predators and highlight the importance of beavers in creating open water areas earlier in the season.     

Ecological engineering and aquatic connectivity: a new perspective from beaver‐modified wetlands

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The multiple-wing-hairs gene encodes a novel GBD-FH3 domain-containing protein that functions both prior to and after wing hair initiation

The frizzled signaling/signal transduction pathway controls planar cell polarity (PCP) in both vertebrates and invertebrates. Epistasis experiments argue that in the Drosophila epidermis multiple wing hairs (mwh) acts as a downstream component of the pathway. The PCP proteins accumulate asymmetrically in pupal wing cells where they are thought to form distinct protein complexes. One is located on the distal side of wing cells and a second on the proximal side. This asymmetric protein accumulation is thought to lead to the activation of the cytoskeleton on the distal side, which in turn leads to each cell forming a single distally pointing hair. We identified mwh as CG13913, which encodes a novel G protein binding domain–formin homology 3 (GBD–FH3) domain protein. The Mwh protein accumulated on the proximal side of wing cells prior to hair formation. Unlike planar polarity proteins such as Frizzled or Inturned, Mwh also accumulated in growing hairs. This suggested that mwh had two temporally separate functions in wing development. Evidence for these two functions also came from temperature-shift experiments with a temperature-sensitive allele. Overexpression of Mwh inhibited hair initiation, thus Mwh acts as a negative regulator of the cytoskeleton. Our data argued early proximal Mwh accumulation restricts hair initiation to the distal side of wing cells and the later hair accumulation of Mwh prevents the formation of ectopic secondary hairs. This later function appears to be a feedback mechanism that limits cytoskeleton activation to ensure a single hair is formed.     

Enhanced invertebrate prey production following estuarine restoration supports foraging for multiple species of juvenile salmonids (Oncorhynchus spp.)

Estuaries provide crucial foraging resources and nursery habitat for threatened populations of anadromous salmon. As such, there has been a global undertaking to restore habitat and tidal processes in modified estuaries. The foraging capacity of these ecosystems to support various species of out‐migrating juvenile salmon can be quantified by monitoring benthic, terrestrial, and pelagic invertebrate prey communities. Here, we present notable trends in the availability of invertebrate prey at several sites within a restoring large river delta in Puget Sound, Washington, U.S.A. Three years after the system was returned to tidal influence, we observed substantial additions to amphipod, copepod, and cumacean abundances in newly accessible marsh channels (from 0 to roughly 5,000–75,000 individuals/m²). In the restoration area, terrestrial invertebrate colonization was dependent upon vegetative cover, with dipteran and hymenopteran biomass increasing 3‐fold between 1 and 3 years post‐restoration. While the overall biodiversity within the restoration area was lower than in the reference marsh, estimated biomass was comparable to or greater than that found within the other study sites. This additional prey biomass likely provided foraging benefits for juvenile Chinook, chum, and coho salmon. Primary physical drivers differed for benthic, terrestrial, and pelagic invertebrates, and these invertebrate communities are expected to respond differentially depending on organic matter exchange and vegetative colonization. Restoring estuaries may take decades to meet certain success criteria, but our study demonstrates rapid enhancements in foraging resources understood to be used for estuary‐dependent wildlife.