Soil phosphorus cycling across a 100-year deforestation chronosequence in the Amazon rainforest.

Deforestation of tropical rainforests is a major land use change that alters terrestrial biogeochemical cycling at local to global scales. Deforestation and subsequent reforestation are likely to impact soil phosphorus (P) cycling, which in P-limited ecosystems such as the Amazon basin has implications for long-term productivity. We used a 100-year replicated observational chronosequence of primary forest conversion to pasture, as well as a 13-year-old secondary forest, to test land use change and duration effects on soil P dynamics in the Amazon basin. By combining sequential extraction and P K-edge X-ray absorption near edge structure (XANES) spectroscopy with soil phosphatase activity assays, we assessed pools and process rates of P cycling in surface soils (0-10 cm depth). Deforestation caused increases in total P (135-398 mg kg-1 ), total organic P (Po ) (19-168 mg kg-1 ), and total inorganic P (Pi ) (30-113 mg kg-1 ) fractions in surface soils with pasture age, with concomitant increases in Pi fractions corroborated by sequential fractionation and XANES spectroscopy. Soil non-labile Po (10-148 mg kg-1 ) increased disproportionately compared to labile Po (from 4-5 to 7-13 mg kg-1 ). Soil phosphomonoesterase and phosphodiesterase binding affinity (Km ) decreased while the specificity constant (Ka ) increased by 83%-159% in 39-100y pastures. Soil P pools and process rates reverted to magnitudes similar to primary forests within 13 years of pasture abandonment. However, the relatively short but representative pre-abandonment pasture duration of our secondary forest may not have entailed significant deforestation effects on soil P cycling, highlighting the need to consider both pasture duration and reforestation age in evaluations of Amazon land use legacies. Although the space-for-time substitution design can entail variation in the initial soil P pools due to atmospheric P deposition, soil properties, and/or primary forest growth, the trend of P pools and process rates with pasture age still provides valuable insights.

Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge.

Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.

Perceived Health Benefits of Taijiquan and Qigong.

Background: Taijiquan and qigong are traditional Chinese therapeutic disciplines with several health benefits and the ability to improve the quality of life of their practitioners. As traditional vegetative biofeedback therapies, they can activate functional vegetative changes in the body. These neurovegetative actions have been studied in the last few years to better explain the mechanisms through which these techniques of traditional Chinese medicine work. Primary Study Objective: To support current research, it is important to further explore these neurovegetative actions according to contemporary Chinese medicine models to clarify the mechanisms of their working in light of conventional medical terms. This study aims to explore the health benefits that these practices may produce for practitioners. Methods: 345 taijiquan and qigong practitioners were recruited for this study to assess the perceived health benefits of taijiquan and qigong. We conducted a survey to assist in this purpose. Results: Taijiquan combined with qigong may be more beneficial than taijiquan alone. Additionally, these practices seem to produce notable benefits for anxiety, depression, and other emotional disturbances. They also seem to have positive results in addressing arthritis and pain in the back, shoulder, neck, and knees. In addition, taijiquan and qigong may have benefits in managing several digestive, neurological, cardiovascular, and respiratory diseases, and provide some assistance in the management of some oncologic conditions. Conclusion: Breathing exercises, slow and controlled movement, self-massage, and directed thought are the therapeutic characteristics that allow this wide range of potential, perceived health benefits. More scientific studies are needed to confirm the mechanisms through which taijiquan and qigong may benefit health. However, it is suggested that these techniques may have an impact on health mainly via the modulation of the autonomic nervous system.

Qigong for the Emotional Exhaustion in Nurses: Implications of a Prospective Randomized Controlled Trial in the COVID-19 Pandemic.

Introduction: Burnout is commonly understood as resulting from chronic stress at work. It may have several consequences for the well-being and health of the worker. As a dimension of burnout, emotional exhaustion appears to be predicted mostly by work overload, interpersonal conflicts, and the inadequate use of skills. Emotional exhaustion is considered to be the affective component of burnout and may cause depersonalization. Burnout seems to be highly prevalent among nurses and more so during the COVID-19 pandemic. To address the new demands that the pandemic has placed on health care systems, nurses must be provided specific training in stress coping techniques. Qigong is an applied psychophysiological feedback technique that can be done independently by the practitioner; it enables the user to learn how to control their bodily functions and processes. As such, the objective of this study is to understand if qigong can be used as a complementary therapy for emotional exhaustion in nurses and if it can be implemented during critical events such as the COVID-19 pandemic. Method: A total of 44 nurses aged between 27 and 54 years (90.9% female), with high levels of emotional exhaustion, were randomized into intervention and control groups. The "white ball" system of qigong, led by a traditional Chinese medicine specialist, was taught to participants in the intervention group for 4 weeks. After this period, participants had 4 weeks for self-practice. The Maslach Burnout Inventory was used to capture the nurses' level of emotional exhaustion at the beginning and end of the experimental period, as well as after the 4-week self-practice period. Results: The results showed that 70% of the participants in the intervention group had significantly decreased emotional exhaustion levels, which reduced from high to either moderate (55%) or low (15%) after the experimental phase. Moreover, these benefits were maintained after the 4 weeks of self practice. Conclusion: The results of this study suggest that qigong may be used as a complementary tool to mitigate burnout (including that induced by COVID-19) among nurses, thus improving health care services and capacity.

Facial nerve dysfunction following parotidectomy: role of intraoperative facial nerve monitoring.

PURPOSE: Facial nerve dysfunction (FND) is a frequent and serious parotidectomy outcome. Intraoperative facial nerve monitoring (IFNM) is an increasingly used technique to identify the facial nerve (FN) and minimize its injury. This study aimed to evaluate the determinant factors in the presence and severity of FND after parotidectomy, including IFNM. STUDY DESIGN, SETTING AND METHODS: A total of 48 patients consecutively submitted to parotidectomy between 2005 and 2020 in a tertiary hospital were retrospectively analyzed. The House-Brackmann Scale (HBS) was used to assess the severity of FND. RESULTS: There was a mean age of 54.2 ± 17.8 years, 50% were male. Pleomorphic adenoma (41.7%) and Warthin's tumor (25.0%) were most common. From the 23 patients (47.9%) who developed some degree of FND (HBS score of 3.41 ± 1.53), 19 (82.6%) showed facial movement recovery, with a mean recovery time of 4.78 ± 2.53 months. IFNM was performed in 39.6% of the surgeries. The use of IFNM (p = 0.514), the type of surgery-partial or total parotidectomy-(p = 0.853) and the type of histology-benign or malignant lesion-(p = 0.852) did not significantly influence the presence of FND in the postoperative period. However, in the subgroup of patients who developed FND, the HBS value was significantly lower in cases of benign pathology (p = 0.002) and in patients who underwent IFNM (p = 0.017), denoting a significantly lower severity. CONCLUSION: In the present study, IFNM and the existence of a benign lesion have been shown to be associated with lower severity of FND.

Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon.

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change.

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world's largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.

Comparison of nasopharyngeal samples for SARS-CoV-2 detection in a paediatric cohort.

AIM: The diagnosis of coronavirus disease 2019 (COVID-19) depends on accurate and rapid testing. Choosing an appropriate sample may impact diagnosis. Naso-oropharyngeal swabs (NOS) are most frequently used, despite several limitations. Since studies suggest nasopharyngeal aspirate (NPA) as a superior alternative in children, we hypothesised collecting both nasopharyngeal swab and aspirate would improve our diagnostic accuracy. METHODS: Observational, longitudinal, prospective study from 7 March to 7 May in a tertiary paediatric hospital in Lisbon. The objective was to compare the rate of detection of SARS-CoV-2 between NOS and NPA samples collected simultaneously. RESULTS: A total of 438 samples collected from 85 patients with confirmed COVID-19. There were 47.7% overall positive specimens - 32% (70/219) positive NOS and 63.5% (139/219) positive NPA. The tests were 67.6% concordant (k = 0.45). 50.3% had positive NPA with negative NOS, while 1.3% had positive NOS with negative NPA. NPA proved to be more sensitive (98.6% with 95% confidence interval 91.2-99.9% vs. 49.6% with 95% confidence interval 41.1-58.2%, P < 0.001). Additionally, the difference between NPA and NOS positive samples was statistically significant across all population groups (age, health condition, clinical presentation, contact with COVID-19 patients or need for hospitalisation), meaning NPA is more sensitive overall. CONCLUSIONS: Nasopharyngeal aspirates had greater sensitivity than naso-oropharyngeal swabs in detecting SARS-CoV-2. Our results suggest paediatric patients would benefit from collecting nasopharyngeal aspirates in hospital settings, whenever feasible, to improve diagnosis of COVID-19.

Assessment of Qigong Effects on Anxiety of High-school Students: A Randomized Controlled Trial.

CONTEXT: Students are vulnerable to developing anxiety, a psychiatric disorder closely related to emotional stress, when systematically stressed by classes, homework, and evaluations. Qigong integrates physical, respiratory, and mental exercises, inducing vegetative biofeedback with significant effects on physiological regulation. OBJECTIVE: The current study aimed to assess the potential effects of specific Qigong exercises on students' anxiety levels and evaluate the feasibility of practical integration in a daily school context. DESIGN: The research team developed a randomized controlled trial. SETTING: This study was performed in Cedros and Horizonte private schools located in Vila Nova de Gaia in Portugal. PARTICIPANTS: Participants were 104 high-school students at the schools. INTERVENTION: Participants were randomly divided into three groups: (1) an intervention group, the Qigong (QG) group (n = 34), which performed Qigong exercises; (2) a control group, the TV documentary (TVD) group (n = 34), which watched a TV documentary; and (3) a second control group, the typical school duties (TSD) group (n = 36), which performed regular school duties. OUTCOME MEASURES: Anxiety levels were assessed through a psychological test, the State-Trait Anxiety Inventory (STAI) and salivary cortisol tests. RESULTS: Psychological and biochemical variables assessed at baseline and postintervention showed a greater decrease in anxiety levels in the QG group than in the other two groups. CONCLUSIONS: Qigong seems to be an efficient tool to reduce anxiety and control the stress of high-school students.

Founder effect of Fabry disease due to p.F113L mutation: Clinical profile of a late-onset phenotype.

BACKGROUND: Knowledge on clinical profiles of late-onset phenotypes of Fabry disease (FD) is essential to better define their natural history. Our study aims to demonstrate a founder effect of FD due to the GLA gene mutation c.337T>C (p.F113L) in the Portuguese region of Guimarães; and to characterize the clinical profile of this late-onset phenotype in a large cohort of genetically related adult patients, living in the same region. METHODS AND RESULTS: FD screening was performed in 150 adult patients with hypertrophic cardiomyopathy (HCM) and found 25 Fabry patients (16.6%). The p.F113L mutation was found in 21 of them, leading to a genealogy study and haplotype analysis of the p.F113L patients. Genealogy research revealed a 12-generation family tree with a common ancestor to p.F113L patients, suggesting a founder effect that was supported by haplotype findings. Pedigree analysis was performed and 120 consecutive p.F113L patients underwent a predefined diagnostic evaluation of FD multiorgan involvement. This late-onset phenotype was characterized by common and/or potentially severe cardiac manifestations (left ventricular hypertrophy 40.8%, atrial fibrillation 5%, non-sustained ventricular tachycardia 12.5%, atrioventricular block 18.3%, bifascicular block 13.4%). Extracardiac manifestations included albuminuria>30 mg/24 h 36.1%, chronic kidney disease≥G3 7.6%, brain white matter lesions 54.4%, stroke 3.3%, sensorineural deafness 44.5%, cornea verticillata 13.9%. Plasma lyso-GB3 was undetectable in females, regardless of clinical manifestations. CONCLUSION: A founder effect of FD due to p.F113L mutation was documented by genealogy and genetics in a Portuguese region. In this late-onset phenotype, although cardiac manifestations carry the highest prognostic impact, extracardiac involvement is common.

Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation.

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (ß-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' ß-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.

Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

Long-term effects of grazing and topography on extra-radical hyphae of arbuscular mycorrhizal fungi in semi-arid grasslands.

Grazing and topography have drastic effects on plant communities and soil properties. These effects are thought to influence arbuscular mycorrhizal (AM) fungi. However, the simultaneous impacts of grazing pressure (sheep ha-1) and topography on plant and soil factors and their relationship to the production of extra-radical AM hyphae are not well understood. Our 10-year study assessed relationships between grazing, plant species richness, aboveground plant productivity, soil nutrients, edaphic properties, and AM hyphal length density (HLD) in different topographic areas (flat or sloped). We found HLD linearly declined with increasing grazing pressure (1.5-9.0 sheep ha-1) in sloped areas, but HLD was greatest at moderate grazing pressure (4.5 sheep ha-1) in flat areas. Structural equation modeling indicates grazing reduces HLD by altering soil nutrient dynamics in sloped areas, but non-linearly influences HLD through plant community and edaphic changes in flat areas. Our findings highlight how topography influences key plant and soil factors, thus regulating the effects of grazing pressure on extra-radical hyphal production of AM fungi in grasslands. Understanding how grazing and topography influence AM fungi in semi-arid grasslands is vital, as globally, severe human population pressure and increasing demand for food aggravate the grazing intensity in grasslands.

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms.

Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane-consuming, rather than methane-producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane-cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities.

The Amazon rainforest is the Earth's largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.

A composite bacteriophage alters colonization by an intestinal commensal bacterium.

The mammalian intestine is home to a dense community of bacteria and its associated bacteriophage (phage). Virtually nothing is known about how phages impact the establishment and maintenance of resident bacterial communities in the intestine. Here, we examine the phages harbored by Enterococcus faecalis, a commensal of the human intestine. We show that E. faecalis strain V583 produces a composite phage (ΦV1/7) derived from two distinct chromosomally encoded prophage elements. One prophage, prophage 1 (ΦV1), encodes the structural genes necessary for phage particle production. Another prophage, prophage 7 (ΦV7), is required for phage infection of susceptible host bacteria. Production of ΦV1/7 is controlled, in part, by nutrient availability, because ΦV1/7 particle numbers are elevated by free amino acids in culture and during growth in the mouse intestine. ΦV1/7 confers an advantage to E. faecalis V583 during competition with other E. faecalis strains in vitro and in vivo. Thus, we propose that E. faecalis V583 uses phage particles to establish and maintain dominance of its intestinal niche in the presence of closely related competing strains. Our findings indicate that bacteriophages can impact the dynamics of bacterial colonization in the mammalian intestinal ecosystem.

THE CONTRIBUTION OF SOIL PHYSICOCHEMICAL PROPERTIES TO THE PRESENCE AND GENETIC DIVERSITY OF BURKHOLDERIA PSEUDOMALLEI.

Burkholderia pseudomallei (Bp), the causative agent of melioidosis, is unevenly distributed in the complex soil environment. Physicochemical factors in the soil have been reported to affect microbial communities in the soil. The effect of physicochemical factors on the number and diversity of organisms in the soil has not been reported. Twenty-five each B. pseudomallei-positive and -negative soil samples were collected from a melioidosis-endemic area. The amount of Bp in each soil sample was measured by culture and quantitative PCR (qPCR). The following physicochemical properties from each soil sample were measured: pH, total organic carbon (TOC), total nitrogen (TN), carbon to nitrogen ratio (C:N ratio), exchangeable calcium (EC) and extractable iron (EI). All the physico- chemical properties measured were significantly different between the Bp-positive and -negative soil samples. The Bp-positive soil samples had lower C:N ratios and lower EC and a higher EI (p < 0.05) than the Bp-negative samples. The average pH was lower (3.7-5.0) in the Bp-negative samples. Among the Bp-positive soil samples, the EC was negatively correlated with the PCR copy number. The amount of bacteria detected with the qPCR method was higher than with the culture method, suggesting the presence of unculturable forms of bacteria that might re-grow when the environmental conditions was suitable. A total of 117 Bp isolates obtained from the soil samples were classified into 25 groups using BOX-PCR. The genetic diversity of Bp, did not correlate with the physicochemical factors investigated. A suitable pH range and C:N ratio may be important for the presence of Bp. The EI supports the needs and EC probably alters the growth of Bp. The genetic diversity of the bacteria was not influenced by the soil factors investigated in this study. This information shows the environment conducive to the growth of Bp. This gives us information about how to potentially control or decrease Bp in the soil in the future.

Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea.

Studying how bacterial strains diverge over space and time and how divergence leads to ecotype formation is important for understanding structure and dynamics of environmental communities. Here we assess the ecological speciation and temporal dynamics of a collection of Shewanella baltica strains from the redox transition zone of the central Baltic Sea, sampled at three time points over a course of 12 years, with a subcollection containing 46 strains subjected to detailed genetic and physiological characterization. Nine clades were consistently recovered by three different genotyping approaches: gyrB gene sequencing, multilocus sequence typing (MLST) and whole genome clustering of data from comparative genomic hybridization, and indicated specialization according to nutrient availability, particle association and temporal distribution. Genomic analysis suggested higher intra- than inter-clade recombination that might result from niche partitioning. Substantial heterogeneity in carbon utilization and respiratory capabilities suggested rapid diversification within the same 'named' species and physical habitat and showed consistency with genetic relatedness. At least two major ecotypes, represented by MLST clades A and E, were proposed based on genetic, ecological and physiological distinctiveness. This study suggests that genetic analysis in conjunction with phenotypic evaluation can provide better understanding of the ecological framework and evolutionary trajectories of microbial species.