Assessing the impact of interfering organic matter on soil metaproteomic workflow

Soil organic matter (SOM) is biologically, chemically, and physically complex. As a major store of nutrients within the soil, it plays an important role in nutrient provision to plants. An enhanced understanding of SOM utilisation processes could underpin better fertiliser management for plant growth, with reduced environmental losses. Metaproteomics can allow the characterisation of protein profiles and could help gain insights into SOM microbial decomposition mechanisms. Here, we applied three different extraction methods to two soil types to recover SOM with different characteristics. Specifically, water-extractable organic matter, mineral-associated organic matter and protein-bound organic matter were targeted with the aim to investigate the metaproteome enriched in those extractions. As a proof-of-concept, replicated extracts from one soil were further analysed for peptide identification using liquid chromatography followed by tandem mass spectrometry. We employed a framework for mining mass spectra for both peptide assignment and fragmentation pattern characterisation. Different extracts were found to exhibit contrasting total protein and humic substance content for the two soils investigated. Overall, water extracts displayed the lowest humic substance content (in both soils) and the highest number of peptide identifications (in the soil investigated) with the most frequent peptide hits associated with diverse substrate/ligand binding proteins of Proteobacteria and derived taxa. Our framework also highlighted a strong peptidic signal in unassigned and unmatched spectra, information that is currently not captured by the pipelines employed in this study. Taken together, this work points to specific areas for optimisation in chromatography and mass spectrometry to adequately characterise SOM-associated metaproteomes.     

Reduced Myxobolus cerebralis Actinospore Production in a Colorado Reservoir May Be Linked to Changes in Tubifex tubifex Population Structure

Abstract

Elucidating the dynamics of a parasitic infection requiring two hosts in a natural ecosystem can be a daunting task. Myxobolus cerebralis (Mc), the myxozoan parasite that causes whirling disease in some salmonids, was detected in the Colorado River upstream of Windy Gap Reservoir (WGR) in 1988. Subsequently, whirling disease was implicated in the decline of wild Rainbow Trout Oncorhynchus mykiss in the river when WGR was identified as a point source of Mc triactinomyxons (TAMs). Between 1997 and 2004, numerous investigations began to elucidate the etiology of Mc in WGR. During this period, Mc TAM production in WGR declined more than 90%. Explanations for the decline have included differences in stream discharge between years, changes in the thermal regime of the lake, severe drought, changes in the fish population structure in WGR, and reductions in the prevalence and severity of Mc infection in salmonids in the Colorado and Fraser rivers upstream of WGR. All of these have been discredited as explanations for the reduced TAM production. In 2005, a new study was conducted to replicate the studies completed in 1998. In this paper, the results of a new real-time polymerase chain reaction assay utilized to quantify the mitochondrial 16S rDNA specific to each of four lineages of Tubifex tubifex in pooled samples of 50 oligochaetes are presented. These results suggest that compared with 1998, the densities of aquatic oligochaetes and T. tubifex have increased, TAM production has been greatly reduced, and the decline is congruent with the dominance of lineages I, V, and VI of T. tubifex—three lineages that are refractory or highly resistant to Mc infection—in the oligochaete population. While it is possible that the resistant lineages function as biofilters that deactivate Mc myxospores, the reason for the decline in TAM production in WGR remains an enigma.

Received February 15, 2012; accepted March 17, 2013     

Ovariectomy as treatment for ovarian bacterial granulomas in a Duvaucel's gecko (Hoplodactylus duvaucelii)

CASE HISTORY: An adult female Duvaucel's gecko (Hoplodactylus duvaucelii) from a threatened species breeding programme presented due to a prolonged gestation period and distended abdomen.

CLINICAL AND PATHOLOGICAL FINDINGS: The gecko was in lean body condition with an irregularly shaped, firm mass in the coelomic cavity. Radiographically there was a diffuse radio-opacity within the coelomic cavity with cranial displacement of the right lung field. Ultrasonography revealed a round homogenous abdominal mass of medium echogenicity with an echogenic capsule. Haematology showed a leucocytosis with a moderate left shift in heterophils and toxic changes. Bilateral ovariectomy was performed to remove two ovarian granulomas and Salmonella enterica subspecies houtenae (IV) was cultured from the ovarian tissue. The gecko recovered well from the surgery, regained weight and remained in good health 3 years following the surgery.

DIAGNOSIS: Pre-ovulatory stasis and ovarian granulomas associated with infection with Salmonella enterica subsp. houtenae.

CLINICAL RELEVANCE: The surgery described in this case resulted in recovery of the gecko, which despite its loss of reproductive capability is of value as an education animal. This is the first report of pre-ovulatory stasis and ovarian granulomas associated with infection with Salmonella enterica in a Duvaucel's gecko and is also the first reported case of pre-ovulatory stasis in a viviparous lizard species. The case adds to knowledge regarding potential reproductive pathology in lizards, which is particularly important information for managers of captive lizard breeding programmes.     

Red urine from red deer grazed on pure red clover swards

Twenty-four red deer hinds with their calves were released on to a newly established pure red clover sward and, 2 days later, red staining of the tail, perineum and hocks was observed. This was presumed to be of urinary origin. Observation of micturition showed that when urine was passed, it was a normal straw colour but it turned scarlet-red about 1 hour after exposure to air. Midstream urine remained the normal colour when held under a pure nitrogen atmosphere immediately after micturition, but it turned red when held in air in the dark, suggesting that the colour change was due to an oxidative rather than a photosensitive reaction. All deer grazing red clover were affected but this did not occur in deer grazing ryegrass/white clover swards. No adverse effects were observed in the deer grazing the red clover, and calf growth was significantly higher than on ryegrass/white clover, suggesting that the red urine had no effect on health or productivity.

Blood and urine analyses showed no signs of haemolysis, haematuria or haemoglobinuria. Preliminary chemical analyses suggest that the compounds involved are not those found in the urine of sheep grazing oestrogenic clover. The nature of the compounds have yet to be determined.     

Determining contemporary and historical sediment sources in a large drainage basin impacted by cumulative effects: the regulated Nechako River,British Columbia,Canada

Purpose

Sediment dynamics in most large river basins are influenced by a variety of different natural and anthropogenic pressures, and disentangling these cumulative effects remains a challenge. This study determined the contemporary and historical sources of fine-grained (<?63-μm) sediment in a large, regulated river basin and linked changes in sources to activities in the basin. The river has seen declines in chinook salmon, sockeye salmon, and the endangered Nechako white sturgeon populations, and sediment (both fine-grained and sands) transport and deposition have been identified as potential causes of these declines.

Materials and methods

Samples of suspended sediment and potential source materials were collected from numerous sites distributed throughout the upper Nechako River Basin in British Columbia, Canada. A floodplain sediment core was also collected in order to reconstruct sediment sources over the last ~?70 years. Discriminating fingerprint properties were used within the MixSIAR model to apportion sources among sub-basins and land-use types. Results were compared to records of precipitation and Nechako River discharge trends, and to changes in landscape development.

Results and discussion

Contributions from the erosion of channel banks dominated the suspended sediment load at most sites. Changes in sediment sources during the 2015 field season reflected snowmelt and patterns of water release from the Nechako Reservoir that affected the sediment-carrying capacity of tributaries and the Nechako River main stem. Spatial variations in 2015 also reflected the distribution of land use (e.g., forested or agricultural land) as well as topography (e.g., slope steepness). Over the last ~?70 years, variations in sediment sources and the characteristics of the sediment (e.g., organic matter content and particle size composition) were linked to the construction of the Kenney Dam (operational in 1954) and the impacts of deforestation by the forestry and agricultural industries. Superimposed on these have been wildfires and a major mountain pine beetle infestation leading to higher erosion rates in the affected areas.

Conclusions

The sediment source fingerprinting technique, in combination with historical information on the hydrometeorology and the land use and river management in the basin, has provided valuable information with which to understand sediment dynamics in the Nechako River Basin. Such an approach can help to disentangle how large river systems respond to a combination of natural and anthropogenic pressures.

     

At sea movement of Macquarie Island giant petrels: Relationships with marine protected areas and Regional Fisheries Management Organisations

Satellite tracking devices were used to examine the at sea movements of southern and northern giant petrels from Macquarie Island during the Austral summers of 2005-06 and 2006-07. Time spent at sea for nine northern giant petrels (four breeding adults, five recently fledged juveniles) and 10 southern giant petrels (three breeding adults, one non-breeding adult, and six recently fledged juveniles) was examined in relation to marine protected areas and fishing activity in the area immediately adjacent to Macquarie Island in 2005-06, and in terms of the jurisdictions of Regional Fisheries Management Authorities (RFMOs) at a broader scale during both seasons. Breeding adult southern and northern giant petrels spent a large proportion of their time at sea in the Macquarie Island Marine Park (25% and 65%, respectively), primarily during chick rearing. Further from Macquarie Island, the most important foraging areas for adult giant petrels were the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) statistical sub-areas 58.4.1 and 88.1, where foraging activity was concentrated around the ice edge and the Polar Frontal Zone. Fledglings of both species spent time in the Marine Park immediately after fledging, before moving into international waters. We found significant temporal and spatial overlap in the areas used by recently fledged juvenile northern giant petrels and the areas utilised by the single trawler that operated in these waters during 2005-06. Adult giant petrels spent little time in RFMO waters other than those under the jurisdiction of CCAMLR, but fledgling southern and northern giant petrels spent considerable time (56% and 78% of total time at sea) on the high seas of the Pacific Ocean, in areas under the jurisdictions of the Commission for the Conservation of Southern Bluefin Tuna (CCSBT), the Western and Central Pacific Fisheries Commission (WCPFC), the Inter American Tropical Tuna Commission (IATTC) and the South Pacific Regional Fisheries Management Organisation (SPRFMO). Band returns indicate that the International Commission for the Conservation of Atlantic Tunas (ICCAT) and the South East Atlantic Fisheries Organisation (SEAFO) areas are likely to be extensively utilised by Macquarie Island giant petrels in the first three years after fledging. Overall, Macquarie Island’s giant petrel populations are well protected by marine reserves during the breeding season. However, after fledging birds move into RFMO areas that currently have low standards of observer coverage and by catch mitigation, and where fisheries related mortality is likely to pose a significant risk.     

Atmospheric CO2 enrichment and nutrient additions to planted soil increase mineralisation of soil organic matter, but do not alter microbial utilisation of plant- and soil C-sources

Plants link atmospheric and soil carbon pools through CO₂ fixation, carbon translocation, respiration and rhizodeposition. Within soil, microbial communities both mediate carbon-sequestration and return to the atmosphere through respiration. The balance of microbial use of plant-derived and soil organic matter (SOM) carbon sources and the influence of plant-derived inputs on microbial activity are key determinants of soil carbon-balance, but are difficult to quantify. In this study we applied continuous ¹³C-labelling to soil-grown Lolium perenne, imposing atmospheric CO₂ concentrations and nutrient additions as experimental treatments. The relative use of plant- and SOM-carbon by microbial communities was quantified by compound-specific ¹³C-analysis of phospholipid fatty acids (PLFAs). An isotopic mass-balance approach was applied to partition the substrate sources to soil respiration (i.e. plant- and SOM-derived), allowing direct quantification of SOM-mineralisation. Increased CO₂ concentration and nutrient amendment each increased plant growth and rhizodeposition, but did not greatly alter microbial substrate use in soil. However, the increased root growth and rhizosphere volume with elevated CO₂ and nutrient amendment resulted in increased rates of SOM-mineralisation per experimental unit. As rhizosphere microbial communities utilise both plant- and SOM C-sources, the results demonstrate that plant-induced priming of SOM-mineralisation can be driven by factors increasing plant growth. That the balance of microbial C-use was not affected on a specific basis may suggest that the treatments did not affect soil C-balance in this study.     

Migration pathways,speed and mortality of Atlantic salmon (Salmo salar) smolts in a Scottish river and the near‐shore coastal marine environment

Long‐distance migration of Atlantic salmon (Salmo salar) is known to result in high levels of mortality. For a species experiencing global population decline, it is thus vital to better understand migration behaviour, both in the river and marine stages. Atlantic salmon smolts (n = 50) were tracked using acoustic telemetry in the River Deveron, Scotland, and adjacent coastal area. Higher rates of mortality were observed in the river (0.77% per km) than the early marine stage of migration (0.0% per km). Mortality likely resulted from predation. Higher swim speeds were recorded in the early marine stage compared with the river (marine = 7.37 ± 28.20 km/day; river = 5.03 ± 1.73 km/day [mean ± SD]), a potential predator avoidance behaviour. The majority of smolts leaving the river did so in darkness and on a flooding tide. Overall river and marine migration success were linked to nights of lower lunar brightness. Marine migration speed decreased with increasing environmental noise levels, a finding with implications for fisheries management. The migration pathway in the early marine environment did not follow obvious geographical features, such as the coastline. Thus, we suggest that early marine environment pathways are more influenced by complex water currents. These findings highlight factors that influence smolt migration survival and behaviour, areas on which future research should focus.     

Diagnostic Methods for Evaluation of Stallion Subfertility: A Review

Classically, evaluation of the breeding stallion for reduced fertility has relied on physical examination of the reproductive system, as well as evaluation of sperm number, motility, and morphology. Over the past 20 years, a number of other diagnostic methods have become available to facilitate reproductive evaluation of the stallion. Specifically, ultrasound imaging has provided much-improved diagnostic methods for evaluation of the external and internal genitalia of the stallion, and these methods have now become routine in evaluation of the stallion. Biochemical analyses of semen can provide useful information for diagnosis of azoospermia (determination of alkaline phosphatase), detection of urine contamination, or changes in pH. Numerous sperm function assays provide information concerning subcellular compartments of the sperm including the plasma membrane, DNA, acrosome, and mitochondria. Data correlating these functional assays with fertility in the stallion are limited in most cases, with the exception of the sperm chromatin structure assay. Finally, the recent sequencing of the equine genome offers the possibility of both marker-assisted selection for fertility traits and more specific information about genetic mutations that may be associated with differing levels of fertility in the stallion.