Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly.

Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model ß-nearest taxon index (ßNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level ßNTI (ßNTIfeat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using ßNTIfeat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that ßNTIfeat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate ßNTIfeat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that ßNTIfeat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.

Intra-Familial Transmission Patterns of COVID-19 Infection among the Rural Residents of Ahmedabad, Gujarat, during an Epidemic of SARS-CoV-2 in India.

We are yet to completely understand the transmission dynamics of coronavirus disease 2019 (COVID-19), a highly infectious disease, and research exploring the same is currently lacking. Hence, a community-based cross-sectional study was conducted to assess the intra-familial transmission pattern of COVID-19 among the rural residents of Ahmedabad, Gujarat, in relation to possible determinants, with a special focus on the viral load as an important factor. This cross-sectional study included visiting 195 families. We interviewed families with at least one case of COVID-19 infection. We recorded information about sociodemographic profiles and secondary transmission of cases. Out of the 195 families, 114 confirmed having at least one infected case within the family. Approximately 38.6% (44/114) of the index cases were asymptomatic, which was much higher than the low viral load index cases. Index cases with high, moderate, and low viral loads had transmitted the infection with an average of 3.3, 1.5, 0.4 secondary cases per index case, respectively. Approximately one-third of the COVID-19 cases were asymptomatic, and the affected individuals were capable of transmitting the disease within families. Moreover, index cases with a higher viral load had a higher transmission potential to generate more secondary cases, as compared to those with a low viral load.

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System.

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

Representing the function and sensitivity of coastal interfaces in Earth system models.

Between the land and ocean, diverse coastal ecosystems transform, store, and transport material. Across these interfaces, the dynamic exchange of energy and matter is driven by hydrological and hydrodynamic processes such as river and groundwater discharge, tides, waves, and storms. These dynamics regulate ecosystem functions and Earth's climate, yet global models lack representation of coastal processes and related feedbacks, impeding their predictions of coastal and global responses to change. Here, we assess existing coastal monitoring networks and regional models, existing challenges in these efforts, and recommend a path towards development of global models that more robustly reflect the coastal interface.

Direct numerical simulation of vortex-induced instability for a zero-pressure-gradient boundary layer.

Vortex-induced instability caused by a free-stream vortical excitation is explored here quantitatively with the help of controlled computational results. First, the computed results are compared with experimental results in Lim et al. [Exp. Fluids 37, 47 (2004)10.1007/s00348-004-0783-5] for the purpose of validation of the three-dimensional (3D) computations. Thereafter, the computed results are explained using methods developed to study nonlinear and spatiotemporal aspects of receptivity and instability for incompressible flows. Here a zero-pressure-gradient (ZPG) boundary layer is perturbed by a constant strength vortex traveling at a fixed height, moving with constant speed, as in the cited experiment. The vortex is created by a translating and rotating circular cylinder in the experiment, with absolute control of the physical parameters. The sign of the translating vortex is fixed by the direction of rotation of the translating cylinder. A high accuracy computing method is employed to solve the 3D Navier-Stokes equation (NSE) for different translation speeds and signs of the free-stream vortex. A nonlinear disturbance enstrophy transport equation (DETE) for incompressible flows is used to explain the vortex-induced instability. This equation is exact and explains the instabilities, as governed by the NSE. The DETE approach has been successfully developed to explain two-dimensional (2D) vortex-induced instability in Sengupta et al. [Phys. Fluids 30, 054106 (2018)10.1063/1.5029560], to trace the linear and nonlinear stages of disturbance growth. Apart from quantification of vortex-induced instability, another major goal is to show how the disturbance evolves from an initial 2D to a 3D stage. While the sign of the translating vortex is important in creating the response field, we additionally highlight the distinct differences caused by increased translation speed and strength of the free-stream vortex on the overall instability. These explain creation of small-scale vortices via the instability of an equilibrium flow, even though the excitation is 2D only. For some cases, this causes 3D bypass transition. We also show a case which demonstrates strong unsteady separation with inflectional velocity profiles, yet the disturbance flow remains essentially 2D, which can be termed a bypass transition.

Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes.

Differentiating the contributions of photosynthesis and respiration to the global carbon cycle is critical for improving predictive climate models. Carbonic anhydrase (CA) activity in leaves is responsible for the largest biosphere-atmosphere trace gas fluxes of carbonyl sulfide (COS) and the oxygen-18 isotopologue of carbon dioxide (CO18O) that both reflect gross photosynthetic rates. However, CA activity also occurs in soils and will be a source of uncertainty in the use of COS and CO18O as carbon cycle tracers until process-based constraints are improved. In this study, we measured COS and CO18O exchange rates and estimated the corresponding CA activity in soils from a range of biomes and land use types. Soil CA activity was not uniform for COS and CO2, and patterns of divergence were related to microbial community composition and CA gene expression patterns. In some cases, the same microbial taxa and CA classes catalyzed both COS and CO2 reactions in soil, but in other cases the specificity towards the two substrates differed markedly. CA activity for COS was related to fungal taxa and ß-D-CA expression, whereas CA activity for CO2 was related to algal and bacterial taxa and α-CA expression. This study integrates gas exchange measurements, enzyme activity models, and characterization of soil taxonomic and genetic diversity to build connections between CA activity and the soil microbiome. Importantly, our results identify kinetic parameters to represent soil CA activity during application of COS and CO18O as carbon cycle tracers.

Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations.

Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative in improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. We present an experimental method, designed to capture sub-surface heterogeneity of an initially homogeneous soil system. This method is based on destructive sampling of a soil lysimeter designed to simulate a small-scale hillslope. A weighing lysimeter of one cubic meter capacity was divided into sections (voxels) and was excavated layer-by-layer, with sub samples being collected from each voxel. The excavation procedure was aimed at detecting the incipient heterogeneity of the system by focusing on the spatial assessment of hydrological, geochemical, and microbiological properties of the soil. Representative results of a few physicochemical variables tested show the development of heterogeneity. Additional work to test interactions between hydrological, geochemical, and microbiological signatures is planned to interpret the observed patterns. Our study also demonstrates the possibility of carrying out similar excavations in order to observe and quantify different aspects of soil-development under varying environmental conditions and scale.

Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing.

The ability of soil to provide ecosystem services is dependent on microbial diversity, with 80-90 % of the processes in soil being mediated by microbes. There still exists a knowledge gap in the types of microorganisms present in soil and how soil management affects them. However, identification of microorganisms is severely limited by classical culturing techniques that have been traditionally used in laboratories. Metagenomic approaches are increasingly becoming common, with current high-throughput sequencing approaches allowing for more in-depth analysis. We conducted a preliminary analysis of bacterial diversity in soils from the longest continuously maintained no-till (NT) plots in the world (52 years) and in adjacent plow-till (PT) plots in Ohio, USA managed similarly except for tillage. Bacterial diversity was determined using a culture-independent approach of high-throughput pyrosequencing of the 16S rRNA gene. Proteobacteria and Acidobacteria were predominant in both samples but the NT soil had a higher number of reads, bacterial richness, and five unique phyla. Four unique phyla were observed in PT and 99 % of the community had relative abundance of <1 %. Plowing and secondary tillage tend to homogenize the soil and reduces the unique (i.e., diverse) microenvironments where microbial populations can reside. We conclude that tillage leads to fewer dominant species being present in soil and that these species contribute to a higher percentage of the total community.

Soluble production and function of vascular endothelial growth factor/basic fibroblast growth factor complex peptide.

Vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) are important proangiogenic factors in tumor procession. The autocrine and paracrine bFGF and the VEGF in tumor tissue can promote tumor angiogenesis, tumor growth, and metastasis. A VEGF/bFGF Complex Peptide (VBP3) was designed on the basis of epitope peptides from both VEGF and bFGF to elicit in vivo production of anti-bFGF and anti-VEGF antibodies. In this study, we reported on the production of recombinant VBP3 using high cell density fermentation. Fed-batch fermentation for recombinant VBP3 production was conducted, and the production procedure was optimized in a 10-L fermentor. The fraction of soluble VBP3 protein obtained reached 78% of total recombinant protein output under fed-batch fermentation. Purified recombinant VBP3 could inhibit tumor cell proliferation in vitro and stimulate C57BL/6 mice to produce high titer anti-VEGF and anti-bFGF antibodies in vivo. A melanoma-grafted mouse model and an immunohistochemistry assay showed that tumor growth and tumor angiogenesis were significantly inhibited in VBP3-vaccinated mice. These results demonstrated that soluble recombinant VBP3 could be produced by large-scale fermentation, and the product, with good immunogenicity, elicited production of high-titer anti-bFGF and anti-VEGF antibodies, which could be used as a therapeutic tumor vaccine to inhibit tumor angiogenesis and tumor growth.

Polycystic ovary syndrome (PCOS) and other androgen excess-related conditions: can changes in dietary intake make a difference?

Polycystic ovary syndrome (PCOS) is a condition that involves the excess production of androgens. It affects up to 10% of all American women and can lead to the development of acne, hirsutism, and infertility. It has also been associated with coronary heart disease, diabetes, and metabolic syndrome. Over half of the women who are diagnosed with PCOS are overweight or obese. Recommendations are made for overweight/obese women to lose weight via diet and exercise. Women with PCOS should also consider maintaining a diet that is patterned after the type 2 diabetes diet. This diet includes an increase in fiber and a decrease in refined carbohydrates, as well as a decrease in trans and saturated fats and an increase in omega-3 and omega-9 fatty acids. Foods that contain anti-inflammatory compounds (fiber, omega-3 fatty acids, vitamin E, and red wine) should also be emphasized. Evidence is provided for the impact of these dietary changes on improvements in the androgen profile of PCOS patients.