Variation of Soil Organic Carbon Density with Plantation Age and Initial Vegetation Types in the Liupan Mountains Areas of Northwest China

Carbon sequestration of plantations formed by three kinds of forestation (natural forest to plantation (NP), grassland to plantation (GP), and cropland to plantation (CP)) greatly depends on the change of soil organic carbon density (SOCD) compared with its initial SOCD before forestation. However, this dependence was rarely studied, especially in semi-humid/arid regions with strong site variation. This limits the precise assessment and management of SOCD. Therefore, the SOCD variations of 0–100 cm soil layers in these three kinds of plantations were studied in the semi-humid/arid Liupan Mountains in northwestern China. The NP with high initial SOCD showed firstly a decrease and then an increase of SOCD up to 293.2 t·ha−1 at 40 years. The CP and GP with low and relatively high initial SOCD showed negligible and slight SOCD decrease after forestation, but then an increase up to 154.5 and 266.5 t·ha−1 at 40 years. After detecting the main factors influencing SOCD for each forestation mode, statistic relationships were fitted for predicting SOCD variation. This study indicates that besides forest age and biomass growth, the effects of initial vegetation, site-dependent initial SOCD, and SOCD capacity, also precipitation and air temperature in some cases, should be considered for more precise assessment and management of SOCD of plantations.

A novel wastewater-based epidemiology indexing method predicts SARS-CoV-2 disease prevalence across treatment facilities in metropolitan and regional populations

There is a need for wastewater based epidemiological (WBE) methods that integrate multiple, variously sized surveillance sites across geographic areas. We developed a novel indexing method, Melvin’s Index, that provides a normalized and standardized metric of wastewater pathogen load for qPCR assays that is resilient to surveillance site variation. To demonstrate the utility of Melvin’s Index, we used qRT-PCR to measure SARS-CoV-2 genomic RNA levels in influent wastewater from 19 municipal wastewater treatment facilities (WWTF’s) of varying sizes and served populations across the state of Minnesota during the Summer of 2020. SARS-CoV-2 RNA was detected at each WWTF during the 20-week sampling period at a mean concentration of 8.5 × 104 genome copies/L (range 3.2 × 102–1.2 × 109 genome copies/L). Lag analysis of trends in Melvin’s Index values and clinical COVID-19 cases showed that increases in indexed wastewater SARS-CoV-2 levels precede new clinical cases by 15–17 days at the statewide level and by up to 25 days at the regional/county level. Melvin’s Index is a reliable WBE method and can be applied to both WWTFs that serve a wide range of population sizes and to large regions that are served by multiple WWTFs.

The evolution of splicing: transcriptome complexity and transcript distances implemented in TranD

Alternative splicing contributes to organismal complexity. Comparing transcripts between and within species is an important first step toward understanding questions about how evolution of transcript structure changes between species and contributes to sub-functionalization. These questions are confounded with issues of data quality and availability. The recent explosion of affordable long read sequencing of mRNA has considerably widened the ability to study transcriptional variation in non-model species. In this work, we develop a computational framework that uses nucleotide resolution distance metrics to compare transcript models for structural phenotypes: total transcript length, intron retention, donor/acceptor site variation, alternative exon cassettes, alternative 5'/3' UTRs are each scored qualitatively and quantitatively in terms of number of nucleotides. For a single annotation file, all differences among transcripts within a gene are summarized and transcriptome-level complexity metrics: number of variable nucleotides, unique exons per gene, exons per transcript, and transcripts per gene are calculated. To compare two transcriptomes on the same co-ordinates, a weighted total distance between pairs of transcripts for the same gene is calculated. The weight function proposed has larger penalties for intron retention and exon skipping than alternative donor/acceptor sites. Minimum distances can be used to identify both transcript pairs and transcripts missing structural elements in either of the two annotations. This enables a broad range of functionality from comparing sister species to comparing different methods of building and summarizing transcriptomes. Importantly, the philosophy here is to output metrics, enabling others to explore the nucleotide-level distance metrics. Single transcriptome annotation summaries and pairwise comparisons are implemented in a new tool, TranD, distributed as a PyPi package and in the open-source web-based Galaxy (www.galaxyproject.org) platform.

Growth and Space-use of Eastern Red-backed Salamanders (Plethodon cinereus) in Mature and Regenerating Forests

Movement and demographic rates are critical to the persistence of populations in space and time. Despite their importance, estimates of these processes are often derived from a limited number of populations spanning broad habitat or environmental gradients. With increasing appreciation of the role fine-scale environmental variation in microgeographic adaptation, there is need and value to assessing within-site variation in movement, growth, and demographic rates. In this study, we analyze three years of spatial capture-recapture data collected from a mixed-use deciduous forest site in central Ohio, USA. Study plots were situated in mature forest on a slope and in successional forest on a ridge but were separated by less than 100-m distance. Our data showed that the density of salamanders was less on ridges, which corresponded with greater distance between nearest neighbors, less overlap in core use areas, greater space-use, and greater shifts in activity centers when compared to salamander occupying the slope habitat. However, these differences were moderate. In contrast, we estimated growth rates of salamanders occupying the ridge to be significantly greater than salamander on the slope. These differences result in ridge salamanders reaching maturity more than one year earlier than slope salamanders, increasing their lifetime fecundity by as much as 43%. The patterns we observed in space use and growth are likely the result of density-dependent processes, reflecting differences in resource availability or quality. Our study highlights how fine-scale, within-site, variation can shape population demographics. As research into the demographic and population consequences of climate change and habitat loss and alteration continue, future research should take care to acknowledge the role that fine-scale variation may play, especially for organisms with small home ranges or limited vagility.

Local biodiversity change reflects interactions among changing abundance, evenness and richness

Biodiversity metrics often integrate data on the presence and abundance of multiple species. Yet our understanding of how changes to the numbers of individuals, the evenness of species relative abundances, and the total number of species covary remains limited, both theoretically and empirically. Using individual-based rarefaction curves, we first show how expected positive relationships among changes in abundance, evenness and richness arise, and how they can break down. We then examined the interdependency between changes in abundance, evenness and richness more than 1100 assemblages sampled either through time or across space. As expected, richness changes were greatest when abundance and evenness changed in the same direction, whereas countervailing changes in abundance and evenness acted to constrain the magnitude of changes in species richness. Site-to-site variation in diversity was greater than rates of change through time. Moreover, changes in abundance, evenness, and richness were often spatially decoupled, and pairwise relationships between changes in these components were weak between sites. In contrast, changes in species richness and relative abundance were strongly correlated for assemblages sampled through time, meaning temporal changes in local biodiversity showed greater inertia and stronger relationships between the components changes when compared to site-to-site variation. Both temporal and spatial variation in local assemblage diversity were rarely attributable solely to changes in assemblage size sampling more or less of a static species abundance distribution. Instead, changing species relative abundances often dominate local variation in diversity. Moreover, how these altered patterns of relative abundance combine with changes to total abundance strongly determine the magnitude of richness changes. Interdependencies found here suggest looking beyond changes in abundance, evenness and richness as separate responses offering unique insights into diversity change can increase our understanding of biodiversity change.

The initial effects of microclimate and invertebrate exclusion on multi-site variation in the mass loss of temperate pine and oak deadwoods

Quantifying deadwood decomposition is prioritized by forest ecologists; nonetheless, uncertainties remain for its regional variation. This study tracked variations in deadwood decomposition of Korean red pine and sawtooth oak in three environmentally different regions of the Republic of Korea, namely western, eastern, and southern regions. After 24 months, dead pine and oak woods lost 47.3 ± 2.8% and 23.5 ± 1.6% in the southern region, 13.3 ± 2.6% and 20.2 ± 2.8% in the western region, and 11.9 ± 7.9% and 13.9 ± 2.3% in the eastern region, respectively. The regional variation in the decomposition rate was significant only for dead pine woods (P < 0.05). Invertebrate exclusion treatment reduced the decomposition rate in all region, and had the greatest effect in the southern region where warmer climate and concentrated termite colonization occurred. The strongest influential factor for the decomposition of dead pine woods was invertebrate exclusion (path coefficient: 0.63). Contrastingly, the decomposition of dead oak woods was highly controlled by air temperature (path coefficient: 0.88), without significant effect of invertebrate exclusion. These findings reflect the divergence in regional variation of deadwood decomposition between pine and oak, which might result from the different sensitivity to microclimate and decomposer invertebrates.

Quality Assessment of an Antimicrobial Resistance Surveillance System in a Province of Nepal

Antimicrobial resistance (AMR) is a global problem, and Nepal is no exception. Countries are expected to report annually to the World Health Organization on their AMR surveillance progress through a Global Antimicrobial Resistance Surveillance System, in which Nepal enrolled in 2017. We assessed the quality of AMR surveillance data during 2019–2020 at nine surveillance sites in Province 3 of Nepal for completeness, consistency, and timeliness and examined barriers for non-reporting sites. Here, we present the results of this cross-sectional descriptive study of secondary AMR data from five reporting sites and barriers identified through a structured questionnaire completed by representatives at the five reporting and four non-reporting sites. Among the 1584 records from the reporting sites assessed for consistency and completeness, 77–92% were consistent and 88–100% were complete, with inter-site variation. Data from two sites were received by the 15th day of the following month, whereas receipt was delayed by a mean of 175 days at three other sites. All four non-reporting sites lacked dedicated data personnel, and two lacked computers. The AMR surveillance data collection process needs improvement in completeness, consistency, and timeliness. Non-reporting sites need support to meet the specific requirements for data compilation and sharing.