Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs

Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.

Evaluating soil loss under land use management and extreme rainfall

Topsoil loss is a widespread environmental concern causing adverse impacts on natural and human systems. Severe weather accompanied with human activities can exacerbate this issue degrading soil health and consequently accelerating global and regional food insecurity. Erosion impairs soil physical and chemical properties such as infiltration rate, water holding capacity, loss of nutrients including soil carbon and nitrogen. Although, temporal properties of a rainfall event have meaningful implications, spatial heterogeneity of a rainfall contributes substantially and cannot be overlooked. Therefore, in this study, we investigated soil loss using weather radar NEXRAD data. We developed extreme rainfall (ER) scenarios and land use practices (nomgt, S0, S1, S2, and S3) and evaluated the watershed response. We found that grazing can manifold soil loss, and if accompanied with extreme rainfalls, soil loss accelerates impacting different subbasins each time. Our results suggest that spatial heterogeneity of ERs can be more significant in individual extreme rainfalls, however, over a year, soil moisture and type of the management practices (grazing and farming) could contribute more to topsoil loss. We classified watershed subbasins into different classes of soil loss severity to determine the soil loss hotspots. Soil loss can go as high as 350 (ton/ha/yr) under the ERs. Land use practices can increase erosion by 3600%. Slight increase in rainfall concentration (S1) can put vulnerable subbasins in extremely severe class (>150 ton/ha/yr). Under moderate increase in the rainfall concentration (S2) more subbasins fall into extremely severe category yielding approximately 200 ton/ha/yr. Under high increase in rainfall concentration (S3) almost all the subbasins fall into the extremely severe class yielding >200 ton/ha/yr. We found that in vulnerable subbasins, up to 10% increase in (Concentration Ratio Index) CI can increase annual soil loss up to 75%. Single ER can generate up to 35% of annual soil loss. Under one ER event soil loss hotspot subbasins can lose up to 160 ton/ha/day. 32% and 80% increase in rainfall amount for an ER event can increase soil loss by 94% and 285% respectively. The results, also, reveal that grazing and farming can be responsible for up 50% of soil loss. Our findings indicate the importance of site-specific managements to mitigate soil loss and all the consequences. Our study can help in better soil loss management implementation. Insights of our study may also help in water quality control and flood mitigation planning efforts.

Assess long-term As, Pb and Cr contamination and uptake by Eriocaulon decangulare in the Apalachicola National Forest

Phytoremediation is an effective remediation process for heavy metal contamination. The primary zone of phytoremediation is the rhizosphere where the plants uptake the heavy metals from the soil matrix. The bioavailability of the contaminants in the rhizosphere is affected by the physical, chemical, and biological conditions of the rhizosphere. In the study area of the Apalachicola National Forest, the concentrations of As, Pb and Cr in the bulk soil (n = 20) were 515.81, 220.77, and 2.02 mg/kg soil, respectively. Using a sequential extraction method, the bioavailability of heavy metals in the bulk soil (S-NR) and rhizosphere soil (S-R) was characterized. The results showed that the bioavailability of the three heavy metals had the order of Cr > Pb > As for S-NR and Pb > As > Cr for S-R. The bioavailability of these metals was affected by the nature of the heavy metals and the soil physicochemical properties. Native plant Eriocaulon decangulare could uptake a large number of heavy metals from the natural soil, demonstrating great phytoremediation potential for metal contamination. Energy Dispersive Spectroscopy (EDS) mapping successfully located the dominant accumulation of heavy metals in aerial parts of E. decangulare. E. decangulare was also found to be highly selective and Pb and As were both extensively accumulated in the shoots and roots. Cr was significantly immobilized in the rhizosphere soil, and also accumulated in the root of E. decangulare. This study not only correlated the phytoremediation potential with heavy metal bioavailability and soil physicochemical properties, but also demonstrated the important role of the nature of heavy metals played during the phytoremediation.

Reduction and bacterial adsorption of dissolved mercuric ion by indigenous bacteria at the Oak Ridge Reservation site

Mercury exists in various forms in the environment and the indigenous bacteria mediated processes have the potential to be used for mercury remediation. In this study, two mixed cultures of indigenous bacteria at the Oak Ridge Reservation site (i.e., ORR soil culture and ORR sediment culture) were selected to study the microbial mediated mercuric reduction under an aerobic condition as well as mercury adsorption onto bacterial surfaces. PCR analysis was performed to provide insights into the microbial community. The mercuric volatilizing experiment demonstrated the mercuric reducing capacity for both ORR cultures, in which the Pseudomonas genus was the dominating Hg⁰ producer. The investigation of the impact of the sole carbon source revealed the energy-dependent characteristics of the mercuric reduction in this study. Namely, the mercuric reduction was nearly not impacted by the type of carbon source but positively related to the energy that a unit amount of substrate could provide. The study also indicated that the mercury adsorption competed with the reduction. According to the fitting of the Langmuir isotherm, the ORR soil culture was found to have a higher mercury adsorption capacity (i.e., 67.5 mg Hg/g dry biomass) than the ORR sediment culture (i.e., 53.1 mg Hg/g dry biomass). The negative correlation between the reduced mercury mass and adsorbed mercury mass was identified for both ORR cultures.

Lead metal biosorption and isotherms studies by metal-resistant Bacillus strain MRS-2 bacterium

In this study, lead (Pb) biosorption studies in aqueous solution were performed with metal-resistant Bacillus strain MRS-2 (ATCC 55674) bacterium which was previously isolated from wastewater plant. It showed minimum inhibition concentration of 300 ppm Pb on the nutrient agar plates. Pb biosorption using MRS-2 bacteria was investigated under different parameters such as pH, temperature, biomass dosage, initial Pb concentration, contact time, and type of biomass by batch experiments. Pb concentration was analyzed through Inductively coupled plasma-optical emission spectrometry. The rate of biosorption (Q) and Pb biosorption capacity (q_e ) were calculated for above mentioned parameters. It was observed that Pb precipitates by itself from the solution at pH 2 and 8 or above without bacteria and precipitation did not increase even in the presence of bacteria. The results showed that the highest biosorption rate and biosorption capacity (mg/g) were observed at pH 7, 25°C, 2-h contact time with live bacteria. The highest biosorption rate was observed at 1.5 g/L biomass dose and 5 ppm initial Pb concentration, whereas the highest Pb biosorption capacity was observed at 0.25 g/L biomass dose and 12.5 ppm initial Pb concentration. It was observed that Pb biosorption by live bacteria occurred through adsorption on cell surface. In this study, the biosorption isotherm analysis favored the Langmuir isotherm model indicating monolayer biosorption. This Bacillus strain showed higher Pb biosorption capacity than most of the previously reported Bacillus strains. In conclusion, this study indicates that the Bacillus MRS-2 strain can be used to remove Pb from industrial wastewaters in an ecofriendly approach.

Skeletal Muscle Protein Composition Adaptations to 10 Weeks of High-Load Resistance Training in Previously-Trained Males

While high-load resistance training increases muscle hypertrophy, the intramuscular protein responses to this form of training remains largely unknown. In the current study, recreationally resistance-trained college-aged males (N = 15; mean ± SD: 23 ± 3 years old, 6 ± 5 years training) performed full-body, low-volume, high-load [68–90% of one repetition maximum (1RM)] resistance training over 10 weeks. Back squat strength testing, body composition testing, and a vastus lateralis biopsy were performed before (PRE) and 72 h after the 10-week training program (POST). Fiber type-specific cross-sectional area (fCSA), myofibrillar protein concentrations, sarcoplasmic protein concentrations, myosin heavy chain and actin protein abundances, and muscle tissue percent fluid were analyzed. The abundances of individual sarcoplasmic proteins in 10 of the 15 participants were also assessed using proteomics. Significant increases (p < 0.05) in type II fCSA and back squat strength occurred with training, although whole-body fat-free mass paradoxically decreased (p = 0.026). No changes in sarcoplasmic protein concentrations or muscle tissue percent fluid were observed. Myosin heavy chain protein abundance trended downward (−2.9 ± 5.8%, p = 0.069) and actin protein abundance decreased (−3.2 ± 5.3%, p = 0.034) with training. Proteomics indicated only 13 sarcoplasmic proteins were altered with training (12 up-regulated, 1 down-regulated, p < 0.05). Bioinformatics indicated no signaling pathways were affected, and proteins involved with metabolism (e.g., ATP-PCr, glycolysis, TCA cycle, or beta-oxidation) were not affected. These data comprehensively describe intramuscular protein adaptations that occur following 10 weeks of high-load resistance training. Although previous data from our laboratory suggests high-volume resistance training enhances the ATP-PCr and glycolytic pathways, we observed different changes in metabolism-related proteins in the current study with high-load training.

An optimized procedure for isolation of rodent and human skeletal muscle sarcoplasmic and myofibrillar proteins

Several published protocols exist for isolating contractile or myofibrillar (MF) proteins from skeletal muscle, however, achieving complete resuspension of the myofibril pellet can be technically challenging. We performed several previously published MF isolation methods with the intent of determining which method was most suitable for MF protein isolation and solubilization. Here, we provide an optimized protocol to isolate sarcoplasmic and solubilized MF protein fractions from mammalian skeletal muscle suitable for several downstream assays.

Skeletal Muscle Myofibrillar Protein Abundance Is Higher in Resistance-Trained Men, and Aging in the Absence of Training May Have an Opposite Effect

Resistance training generally increases skeletal muscle hypertrophy, whereas aging is associated with a loss in muscle mass. Interestingly, select studies suggest that aging, as well as resistance training, may lead to a reduction in the abundance of skeletal muscle myofibrillar (or contractile) protein (per mg tissue). Proteomic interrogations have also demonstrated that aging, as well as weeks to months of resistance training, lead to appreciable alterations in the muscle proteome. Given this evidence, the purpose of this small pilot study was to examine total myofibrillar as well as total sarcoplasmic protein concentrations (per mg wet muscle) from the vastus lateralis muscle of males who were younger and resistance-trained (denoted as YT, n = 6, 25 ± 4 years old, 10 ± 3 self-reported years of training), younger and untrained (denoted as YU, n = 6, 21 ± 1 years old), and older and untrained (denoted as OU, n = 6, 62 ± 8 years old). The relative abundances of actin and myosin heavy chain (per mg tissue) were also examined using SDS-PAGE and Coomassie staining, and shotgun proteomics was used to interrogate the abundances of individual sarcoplasmic and myofibrillar proteins between cohorts. Whole-body fat-free mass (YT > YU = OU), VL thickness (YT > YU = OU), and leg extensor peak torque (YT > YU = OU) differed between groups (p < 0.05). Total myofibrillar protein concentrations were greater in YT versus OU (p = 0.005), but were not different between YT versus YU (p = 0.325). The abundances of actin and myosin heavy chain were greater in YT versus YU (p < 0.05) and OU (p < 0.001). Total sarcoplasmic protein concentrations were not different between groups. While proteomics indicated that marginal differences existed for individual myofibrillar and sarcoplasmic proteins between YT versus other groups, age-related differences were more prominent for myofibrillar proteins (YT = YU > OU, p < 0.05: 7 proteins; OU > YT = YU, p < 0.05: 11 proteins) and sarcoplasmic proteins (YT = YU > OU, p < 0.05: 8 proteins; OU > YT&YU, p < 0.05: 29 proteins). In summary, our data suggest that modest (~9%) myofibrillar protein packing (on a per mg muscle basis) was evident in the YT group. This study also provides further evidence to suggest that notable skeletal muscle proteome differences exist between younger and older humans. However, given that our n-sizes are low, these results only provide a preliminary phenotyping of the reported protein and proteomic variables.

Muscle fiber hypertrophy in response to 6 weeks of high-volume resistance training in trained young men is largely attributed to sarcoplasmic hypertrophy

Cellular adaptations that occur during skeletal muscle hypertrophy in response to high-volume resistance training are not well-characterized. Therefore, we sought to explore how actin, myosin, sarcoplasmic protein, mitochondrial, and glycogen concentrations were altered in individuals that exhibited mean skeletal muscle fiber cross-sectional area (fCSA) hypertrophy following 6 weeks of high-volume resistance training. Thirty previously resistance-trained, college-aged males (mean ± standard deviation: 21±2 years, 5±3 training years) had vastus lateralis (VL) muscle biopsies obtained prior to training (PRE), at week 3 (W3), and at week 6 (W6). Muscle tissue from 15 subjects exhibiting PRE to W6 VL mean fCSA increases ranging from 320–1600 μm² was further interrogated using various biochemical and histological assays as well as proteomic analysis. Seven of these individuals donated a VL biopsy after refraining from training 8 days following the last training session (W7) to determine how deloading affected biomarkers. The 15 fCSA hypertrophic responders experienced a +23% increase in mean fCSA from PRE to W6 (p<0.001) and, while muscle glycogen concentrations remained unaltered, citrate synthase activity levels decreased by 24% (p<0.001) suggesting mitochondrial volume decreased. Interestingly, repeated measures ANOVAs indicated that p-values approached statistical significance for both myosin and actin (p = 0.052 and p = 0.055, respectively), and forced post hoc tests indicated concentrations for both proteins decreased ~30% from PRE to W6 (p<0.05 for each target). Phalloidin-actin staining similarly revealed actin concentrations per fiber decreased from PRE to W6. Proteomic analysis of the sarcoplasmic fraction from PRE to W6 indicated 40 proteins were up-regulated (p<0.05), KEGG analysis indicated that the glycolysis/gluconeogenesis pathway was upregulated (FDR sig. <0.001), and DAVID indicated that the following functionally-annotated pathways were upregulated (FDR value <0.05): a) glycolysis (8 proteins), b) acetylation (23 proteins), c) gluconeogenesis (5 proteins) and d) cytoplasm (20 proteins). At W7, sarcoplasmic protein concentrations remained higher than PRE (+66%, p<0.05), and both actin and myosin concentrations remained lower than PRE (~-50%, p<0.05). These data suggest that short-term high-volume resistance training may: a) reduce muscle fiber actin and myosin protein concentrations in spite of increasing fCSA, and b) promote sarcoplasmic expansion coincident with a coordinated up-regulation of sarcoplasmic proteins involved in glycolysis and other metabolic processes related to ATP generation. Interestingly, these effects seem to persist up to 8 days following training.

Bacterial-facilitated uranium transport in the presence of phytate at Savannah River Site

At the Department of Energy (DOE) managed Savannah River Site (SRS), uranium and other heavy metals continue to pose threats to the ecosystem health and processes. In the oxic soil of this site, uranium is present primarily as soluble salts of the uranyl ion (i.e., U(VI) or UO₂²⁺). Although UO₂²⁺ has a strong sorption to the soil, the mobile indigenous bacteria may facilitate its transport. On the contrary, precipitation of UO₂²⁺ with phosphate has been found to be an alternative remediation strategy. This research investigated the effects of mobile bacteria and phytate on UO₂²⁺ transport at SRS in column experiments. It was discovered that UO₂²⁺ can barely be mobilized by de-ionized water but can be significantly transported with the aid of mobile indigenous bacteria. UO₂²⁺ had the most facilitated transport observation when it reached equilibrium with the bacteria before the transport. When UO₂²⁺ and bacterial were introduced to the soil at the same time or UO₂²⁺ was pre-deposited in the soil, the facilitated transport was less pronounced. In the presence of phytate, bacterial-facilitated UO₂²⁺ transport was hindered. pH was found to play the key role for UO₂²⁺ immobilization in the presence of phytate. The immobilization of UO₂²⁺ with the addition of phytate increased with the increase of pH within the pH range of this study because of the impact of pH on the solubility of UO₂(OH)₂. Phytate promoted UO₂^--PO₄^3- complex and/or [Ca(UO₂)₂(PO₄)₂] formation, leading to enhanced UO₂²⁺ immobilization in the SRS soil.

Sequential anaerobic-aerobic degradation of munitions waste

A sequential anaerobic-aerobic biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was studied. The results demonstrated that: (i) a complete degradation of RDX was achieved within 20 days using a consortium of bacteria from a wastewater activated sludge, (ii) RDX degradation did not occur under aerobic conditions alone, (iii) RDX-degrading bacterial strain that was isolated from the activated sludge completely degraded RDX within 2 days, and (iv) RDX- induced protein expressions were observed in the RDX-degrading bacterial strain. Based on fatty acid composition and a confirmation with a 16S rRNA analysis, the RDX-degrading bacterial strain was identified as a Bacillus pumilus-GC subgroup B.