Changes In Abundance Research Articles

Trimethylamine‐N‐Oxide regulates cognitive function in Alzheimer’s Disease patients and mice model through brain‐gut‐microbiota axis

AbstractBackgroundThe regulatory role of Trimethylamine‐N‐oxide (TMAO) for cognition from the perspective of microbiota‐gut‐brain (MGB) axis in AD remains unclear.MethodIn clinical cohort study for effects of 24‐week computerized cognitive training (CCT), registered on clinicaltrials.gov (NCT06094452), plasma TMAO levels were quantified using ELISA in MCI (n=39) and mild AD patients (n=35). Correlation analyses were conducted to assess the relationship between changes in TMAO levels and cognitive function (ADAS‐cog score) and gut microbiota indices. In animal model experiments, C57/BL6 aged mice and APP/PS1 transgenic mice were administrated by water feeding with 1.2% TMAO for 16 weeks and 1.0% of its inhibitor 3,3‐Dimethyl‐1‐butanol (DMB) for 8 weeks. TMAO levels in plasma and cerebrospinal fluid (CSF) were measured by ELISA. Cerebral blood flow (CBF) activation was detected by a laser speckle imaging system. Cognitive behavior was evaluated using Morris Water Maze test. The expressions of BBB function proteins (ZO‐1, Occludin, and PDGFRβ,) and neuroinflammatory markers (HMGB1 and IL‐1β) were detected by western blotting. The deposition of β‐amyloid (Aβ) plaques and neuronal survival in hippocampus were visualized by histochemical and Nissl staining.ResultTMAO was significantly increased in plasma of AD patients. After CCT intervention, TMAO was significantly decreased in the CCT group, and this decrease was positively correlated with ADAS‐cog (r=0.549), and negatively correlated with Shannon evenness (r= ‐0.372). TMAO changes were also negatively correlated with the relative abundance change of Roseburia (r=‐0.443), Lachnospiraceae_UCG‐004 (r=‐0.392), and Lactobacillus (r=0.480), while positively correlated with Ruminococcus_torgues (r=0.443), Fusobacterium (r=0.484) and Herbasporillum (r=0.365). In animal models, TMAO was increased in the plasma and CSF of APP/PS1 mice. After supplemented with 1.2% TMAO, the cognitive performances of C57 and APP/PS1 mice were significantly impaired. The activation amplitude of CBF was decreased, and the expression of BBB function proteins (ZO‐1, Occludin, and PDGFRβ) were significantly decreased. The expressions of neuroinflammation marker HMGB1 and IL‐1β were significantly increased; the accumulation of Aβplaques was increased with decreased neuronal survival. Circulating level of TMAO was decreased after DMB intervention, which showed cognitive protection effects.ConclusionTMAO may be a novel biomarker that regulates cognition of AD through MGB axis.

A Long-duration Superflare on the K Giant HD 251108

Many giant stars are magnetically active, which causes rotational variability, chromospheric emission lines, and X-ray emission. Large outbursts in these emission features can set limits on the magnetic field strength and thus constrain the mechanism of the underlying dynamo. HD 251108 is a Li-rich active K-type giant. We find a rotational period of 21.3 days with color changes and additional long-term photometric variability. Both can be explained with very stable stellar spots. We followed the decay phase of a superflare for 28 days with NICER and from the ground. We track the flare decay in unprecedented detail in several coronal temperature components. With a peak flux around 1034 erg s−1 (0.5–4.0 keV) and an exponential decay time of 2.2 days in the early decay phase, this is one of the strongest flares ever observed, yet it follows trends established from samples of smaller flares, for example, for the relations between Hα and X-ray flux, indicating that the physical process that powers the flare emission is consistent over a large range of flare energies. We estimate a flare loop length about 2–4 times the stellar radius. No evidence is seen for abundance changes during the flare.

Constitutive opening of the Kv7.2 pore activation gate causes KCNQ2-developmental encephalopathy

Pathogenic variants in KCNQ2 encoding Kv7.2 voltage-gated potassium channel subunits cause developmental encephalopathies (KCNQ2-encephalopathies), both with and without epilepsy. We herein describe the clinical, in vitro, and in silico features of two encephalopathy-causing variants (A317T, L318V) in Kv7.2 affecting two consecutive residues in the S6 activation gate that undergoes large structural rearrangements during pore opening; the disease-causing A356T variant in KCNQ3, paralogous to the A317T variant in KCNQ2, was also investigated. Currents through KCNQ2 mutant channels displayed increased density, hyperpolarizing shifts in activation gating, faster activation and slower deactivation kinetics, and resistance to changes in the cellular concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2), a critical regulator of Kv7 channel function; all these features are consistent with a strong gain-of-function effect. An increase in the probability of single-channel opening, with no change in membrane abundance or single-channel conductance, was responsible for the observed gain-of-function effects. All-atom molecular dynamics simulations revealed that the mutations widened the inner pore gate and stabilized a constitutively open channel configuration in the closed state, with minimal effects on the open conformation. Thus, mutation-induced stabilization of the inner pore gate open configuration is a molecular pathogenetic mechanism for KCNQ2-related encephalopathies.

Extent of Benthic Habitat Disturbance by Offshore Infrastructure

The effects of the interaction between sandy, mobile, low-relief (sorted) bedforms and two sewage outfalls were investigated along the south shore of Long Island, NY. Sand bedforms at scales from ripples to ridges are common on continental shelves. In dynamic environments, these features can migrate 10s to 100s of meters per year, especially during storms. Beyond engineering considerations, little is known of the interaction between these mobile features and anthropogenic structures. Modification of bedform topography and sediment grain-size distribution can be expected to alter the species composition, abundance, and diversity of the benthic community. At the study site, the interaction increased the scour of modern fine- to medium-grained sediments extending out to a kilometer and uncovered coarser-grained late Pleistocene sediments. This alteration of the seafloor in turn resulted in changes in composition, higher abundance, and lower diversity in the species assemblage found in the impacted area. The most advantaged species was Pseudunciola obliquua, a sightless, tube-building, surface deposit-feeding amphipod that is known to prefer a dynamic coarse sand habitat. Overall, the ecological effects of artificial structures on a wave-dominated seabed with sorted bedforms have not been adequately assessed. In particular, and of great importance, is the pending large-scale development of wind farms off the East Coast of the U.S.

Assessing the long-term survival of bakanae pathogen Fusarium fujikuroi in rice-wheat cropping system in Northern - India using advanced metagenomic and qPCR techniques

Bakanae disease, caused by Fusarium fujikuroi, is emerging as a major threat to rice crops worldwide, posing a significant challenge to basmati rice farming in India. The difficulty in managing the disease is compounded by the morphological similarities between various pathogenic species and the limited research on its soil-borne nature, especially in the context of Indian farming conditions. This study utilized quantitative PCR (qPCR) and metagenomic approaches to monitor Fusarium fujikuroi population in soil from a rice-wheat cropping system during 2021–22 in North Indian conditions. The qPCR analysis revealed changes in Fusarium fujikuroi abundance, with the highest colonization in August 2021 (1.19 × 1010) and a notable decline by June 2022 (1.84 × 106). Metagenomic studies based abundance analysis at the phylum level showed the prevalence of ascomycetes in all the samples taken for the study. The key fungal genera observed in bakanae infected field following rice-wheat cropping system included Talaromyces, Mortierella, Trichoderma, Aspergillus, Penicillium, Emericellopsis, Fusarium, Chaetomium, Westerdykella and Amesia. Talaromyces was most abundant in September 2021 (34.40 %) which corresponded with the lowest Fusarium abundance (0.22 %) in soil samples tested. Other beneficial fungi such as Trichoderma, Penicillium and Westerdykella etc. were also detected during the evaluation, supporting their role in managing bakanae disease. The decrease in the Fusarium fujikuroi population over the study period, as revealed by quantitative PCR and metagenomics, indicates that the viability of Fusarium fujikuroi as a soil-borne pathogen is limited. This suggests the importance of maintaining a proper interval of 6–7 months between harvest and the next sowing. Further, the study emphasized the potential use of biocontrol agents to mitigate bakanae disease problem along with the promotion of sustainable and resilient rice farming systems.

Examination of intestinal microbiota abundance of honey bees supplemented and unsupplemented with probiotic bacteria by QPCR

The aim of this study is to compare the bacterial load in the guts of honey bees supported and unsupplemented with probiotic supplements. To investigate the effects of a commercial bee probiotic containing different Lactobacillus species and different spice extracts on the composition of the gut microbiota of honey bees, QPCR counts of Lactobacillus spp. and Firmicutes phylum gene copies in gut mixtures from 12 different bee groups with and without probiotic supplementation were performed. There was a significant difference between the levels of Lactobacillus spp. in the guts of both groups. When Lactobacillus spp. levels in the guts of honey bees not given probiotics were compared to the Lactobacillus spp. levels in the guts of honey bees given probiotics, it was determined that there was an approximately 5.5-fold difference. However, it was observed that there was no significant difference in the Firmicutes load in the bee guts of both groups. These findings show that the applied probiotic formulation significantly affects the intestinal microbiome of healthy individuals and provides a proportional change in microbial abundance, especially in terms of Lactobacillus spp.

Effects of environmentally relevant concentrations of glyphosate and aminomethylphosphonic acid on biotransformation and stress response proteins in the liver of zebrafish (Danio rerio)

Herbicides pose a threat to various non-target organisms, including fish. A widely used herbicide, glyphosate, and its main breakdown product, aminomethylphosphonic acid (AMPA), are quite ubiquitous in freshwater systems. The aim of this work was to analyze changes in the relative abundance of hepatic proteins participating in the biotransformation and response to chemical stress in adult zebrafish Danio rerio exposed to environmentally relevant concentrations of glyphosate (100 μg/L), AMPA (100 μg/L), and their mixture (50 μg/L + 50 μg/L) for two weeks. Proteomic analysis showed that the tested concentrations caused dysregulation of various biotransformation proteins, the most upregulated of which in all treatment groups was the Phase I enzyme cyp27a7. While glyphosate had a more pronounced impact on the biotransformation pathways, AMPA showed stronger interference with redox homeostasis. When acting together, the parent compound and its metabolite were more potent to disturb fish metabolic processes, including nucleotide metabolism and proteasome pathway, and to downregulate proteins known for their roles in protection from oxidative modifications of cellular constituents and disruption of redox signaling.

Microbiome analysis of serum extracellular vesicles in gestational diabetes patients.

Gestational Diabetes Mellitus (GDM) is among the most common complications during pregnancy, posing serious risks to both the patient's and offspring's health and well-being. Alterations in the maternal microbiome are closely associated with the pathogenesis of GDM, with Extracellular Vesicles (EVs) facilitating communication between microbiota and the host. However, little is known about the relationship between the microbial composition within EVs and the pathogenesis of GDM. Therefore, this study aims to characterize the microbiota within serum EVs of GDM Patients (GDM group) and to identify microbial communities that significantly differ from those in Women With Normal Pregnancies (NonGDM group). Blood samples were collected from both groups of patients, and EVs derived from serum were isolated via centrifugation. Identification and characterization of EVs were performed using transmission electron microscopy and nanoparticle flow cytometry. Microbiome analysis of serum EVs from both groups was conducted using 16S rRNA sequencing. Results indicated altered diversity in microbial communities within serum EVs of GDM patients. Further analysis at the phylum, family, genus, and species levels revealed that Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the dominant taxa in the EVs of both the NonGDM and GDM groups. Specifically, Actinobacteria and Firmicutes showed increased relative abundance in GDM group EVs compared to NonGDM, leading to a higher Firmicutes/Bacteroidetes ratio, while Proteobacteria and Bacteroidetes exhibited decreased relative abundance. Tax4Fun analysis revealed enrichment of microbial functions related to amino acid metabolism, carbohydrate metabolism, energy metabolism, and metabolism of cofactors and vitamins in both patient groups. In conclusion, this study reveals a potential correlation between changes in the microbial composition and diversity of serum EVs and the onset and development of GDM. Furthermore, changes in the relative abundance of Actinobacteria, Proteobacteria,Bacteroidetes, and Firmicutes may play an important role in the pathogenesis of GDM.

The spatiotemporal changes of crab community in the Yangtze River Estuary after the fishing ban

The Yangtze River Estuary is the traditional habitat of fishery resources in China and also one of the crab fishing sites, but nowadays the crab resources have been seriously affected by high-intensity anthropogenic disturbance. To understand the composition and diversity of crab community following the fishing ban, six surveys were conducted from August 2022 to November 2023 using the single-bag trawl method. This study examined the crab community composition, biodiversity, resource density, spatiotemporal distribution patterns, and main influencing factors. Results indicated that a total of 14 crab species lived in the Yangtze River Estuary. Matuta planipes and Portunus trituberculatus were dominant crabs in summer 2022. P. trituberculatus, Eriochier leptognathus, and Charybdis japonica were dominant crabs in autumn 2022. Then, E. leptognathus and Eriocheir sinensis were dominant crabs in winter 2023. Notably, the largest numbers of dominant crabs appeared in spring 2023, including M. planipes, P. trituberculatus, E. leptognathus, C. japonica, and E. sinensis. Three same dominant crabs (M. planipes, P. trituberculatus, C. japonica) were identified in the summer and autumn of 2023. Thereinto, P. trituberculatus was the most dominant crab. The abundance and biomass trends of estuary crabs were winter< spring< autumn< summer. The community diversity index, evenness index, and richness index were winter< summer< autumn< spring, indicating the seasonal changes in abundance, biomass, and biodiversity. Correlation and redundancy analysis revealed that dissolved oxygen and salinity were the most critical environmental factors, which affect the changes in crab community in the estuary. This study revealed the changing characteristics of crab resources in the Yangtze River Estuary after the fishing ban, and provided the essential data and scientific basis for resource conservation and management decisions.

Sprayable Biodegradable Polyester-Urethane-Urea Mulching Treatment Increases Abundance of Soil Microbes

The paper investigates for the first time the impact of a novel sprayable, biodegradable polyester-urethane-urea (PEUU) mulch on the microbial community composition of an agricultural soil. In this study changes to the composition of the soil microbial community and in soil enzyme activity involved in nutrient cycling were monitored on tomato plants grown under controlled greenhouse conditions. Particular attention was given to impacts on the relative changes in abundance of soil microbes. The PEUU mulch reduced the abundance of a small number of soil microbe taxa, but also provided an environment in which some taxa, which were comparatively rare in initial and unmulched soils, thrived. Importantly, the relative abundances of Azospirillum, Noviherbaspirillum, Exophiala, Phoma, Chaetomium and Clonostachys species all increased in soils treated with PEUU mulch. Principal coordinates analysis revealed the microbial community composition on PEUU films alone and in PEUU treated soil were most similar, while the PEUU films’ microbial community differed the most from the initial soil’s microbial community. These results indicate that from an agricultural productivity and an environmental safety standpoint the use of PEUU mulch may be preferable to PE and could provide additional plant growth benefits by increasing the abundance of soil microbes.

Triangle correlations of lung microbiome, host physiology and gut microbiome in a rat model of idiopathic pulmonary fibrosis

Changes in lung and gut microbial communities have been associated with idiopathic pulmonary fibrosis (IPF). This study aimed to investigate correlations between microbial changes in the lung and gut and host physiological indices in an IPF model, exploring potential mechanisms of the lung-gut axis in IPF pathogenesis. IPF model rats were established via trans-tracheal injection of bleomycin, with assessments of hematological indices, serum cytokines, lung histopathology, and microbiome alterations. Significant differences in microbial structure and composition were observed in the IPF model compared to controls, with 14 lung and 7 gut microbial genera showing significant abundance changes. Further analysis revealed 20 significant correlations between pulmonary and gut genera. Notably, 11 pairs of correlated genera were linked to the same IPF-related physiological indices, such as hydroxyproline, mean corpuscular volume (MCV), and red cell distribution width-standard deviation (RDW-SD). We identified 24 instances where a lung and a gut genus were each associated with the same physiological index, forming "lung genus—index—gut genus" relationships. Mediation analysis showed that indices like hydroxyproline, MCV, and RDW-SD mediated correlations between 10 lung genera (e.g., Cetobacterium, Clostridium XVIII ) and the gut genus Allobaculum. This study first describes gut-lung microbial interactions in pulmonary fibrosis. Mediation analysis suggests pathways underlying "lung genus—host index—gut genus" and "gut genus—host index—lung genus" correlations, thus providing clues to further elucidate the mechanisms of the “gut-lung axis” in IPF pathogenesis.

Molecular compositional variation of organic matter deposited on the East Tasman Plateau during the Paleocene–Eocene Thermal Maximum

Molecular compositions in sediments collected by Ocean Drilling Program Leg 189 at Site 1172 in the Tasmanian Gateway, Australia have been characterised by gas chromatography–mass spectrometry to assess the impact of the Paleocene–Eocene Thermal Maximum (PETM) on organic matter origins and evolution. Total organic carbon (TOC) and sulfur contents reach the lowest values immediately before the initiation of the negative carbon isotope excursion (CIE) in the shallow marine environment on the East Tasman Plateau. The TOC content increases slightly while the sulfur content increases more substantially during deposition of the CIE, suggesting the occurrence of low-oxygen environments during the PETM event. The studied section is thermally immature, as shown by the dominance of biological configuration biomarkers such as 17β(H),21β(H)-hopanes (ββ) and hopenes. Changes in relative abundance of compound classes and isomer ratios are largely caused by the variation of source inputs and depositional conditions. Very low abundance of marine steroids during the CIE, but very enriched hopanoids, indicate low marine productivity, in accord with substantial remineralisation of organic matter in the bottom waters. The ββ-hopanes are the most abundant hopanoid series, followed by the neohop-13(18)-ene and hop-17(21)-ene series, further verifying the immaturity of the organic constituents in the samples. Hopane ratios (ββ/(βα + αβ) and βα/(βα + αβ) with different carbon numbers are systematically higher in sediments deposited during the CIE than those formed pre- and post-CIE, suggest increased bacterial inputs. Higher C30/C29 and C30/C31 hopanoid ratios in the CIE sediments are consistent with a greater contribution from in situ bacterial organic matter, rather than continental soil erosion by flooding. This is supported by the higher C27–32 hopanoids/(C27 + C29 + C31n-alkanes) ratio and sulfur content during the CIE. A relatively lower TOC content in the sediments formed during the PETM is inferred to have been caused by dilution by both enhanced detrital input and intensified bacterial consumption. This study demonstrates that the biomarker approach can play an important role in the identification of organic matter origin and characterisation of depositional environment for PETM sequences.

Impacts of a warming climate on the non-breeding distribution of a classic differential migrant

Many changes in species’ geographic distributions have been attributed to recent climate warming. One understudied phenomenon is the effect of climate change on differential migrants, species in which the sexes differ in distance migrated to and from the breeding range. We evaluated the impact of climate change on differential migration in the dark-eyed junco (Junco hyemalis) by assessing temporal and geographic changes in overall population abundance throughout the winter range over the past 60 years. We also compared the abundance of females in two wintering populations studied 15 years ago with historical abundances studied 45 years ago We observed a northward movement of the population as a whole and an increase in female abundance at higher latitudes that correlated with recent changes in winter climate. These findings suggest that climate change has reduced distance migrated in this species and increased the proportion of females wintering at higher latitudes, providing new insights into the impact of climate warming on migratory distance and winter distributions.

Do penguins care about their neighborhood? Population implications of bioerosion in Magellanic penguin, Spheniscus magellanicus, at Martillo Island, Beagle Channel, Argentina.

Intrinsic and extrinsic factors, such as bioerosion at nesting sites, regulate population dynamics and are relevant for the long-term conservation of penguins. Colony trends (between 2004-2022) were studied in a Magellanic penguin colony on Martillo Island, Beagle Channel, Argentina and compared between zones with contrasting degrees of erosion (high, medium, low). Individuals from each zone were characterized for foraging ecology, stress, and reproductive performance during the 2017-2018 breeding season to better understand the colony dynamics. Changes in nest abundance varied in magnitude between nesting zones with different characteristics of occupation time, density and erosion. Declines in nest abundance in the densest, most eroded and longest occupied zone suggests that environmental degradation may be limiting the colony's carrying capacity. A higher percentage of late breeders (probably younger breeders) occupied the less eroded and more recently occupied zone. Foraging, breeding and stress barely differed between zones. New individuals recruiting into the breeding colony select less-eroded zones, either to reduce competition for nests or to avoid other effects of erosion and high-density areas. If this is the mechanism behind the shift in numbers throughout the island, we expect the island to be progressively occupied to the west. If competition or other density dependent factors are at play, a time will come when the vacant east side will begin to be recolonized by younger individuals. However, if erosion or other long-term effects spread throughout the island, recolonization may not occur and the colony may ultimately be abandoned as individuals search for new breeding grounds. Erosion at the breeding site may be a key factor in regional population trends of this burrow nesting species, by following an extinction / colonization of new sites process.

ZTF SN Ia DR2: The spectral diversity of Type Ia supernovae in a volume-limited sample

More than 3000 spectroscopically confirmed Type Ia supernovae (SNe Ia) are presented in the second data release (DR2) of the Zwicky Transient Facility survey. In this paper we detail the spectral properties of 482 SNe Ia near maximum light, up to a redshift limit of z leq 0.06. We measured the velocities and pseudo-equivalent widths (pEW) of key spectral features ( and and investigated the relation between the properties of the spectral features and the photometric properties from the SALT2 light-curve parameters as a function of spectroscopic sub-class. We discuss the non-negligible impact of host galaxy contamination on SN Ia spectral classifications, and we investigate the accuracy of spectral template matching of the DR2 sample. We define a new subclass of underluminous SNe Ia (04gs-like) that lie spectroscopically between normal SNe Ia and transitional 86G-like SNe Ia (stronger than normal SNe Ia, but significantly weaker features than 86G-like SNe). We model these 04gs-like SN Ia spectra using the radiative-transfer spectral synthesis code tardis and show that cooler temperatures alone are unable to explain their spectra; some changes in elemental abundances are also required. However, the broad continuity in spectral properties seen from bright (91T-like) to faint normal SN Ia, including the transitional and 91bg-like SNe Ia, suggests that variations within a single explosion model may be able to explain their behaviour.

In Silico Analysis of Probiotic Bacteria Changes Across COVID-19 Severity Stages.

The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are symbionts of the gut microbiota and contribute to host health. However, comparing results across studies is challenging due to differences in analysis methods and reference databases. We screened 16S rRNA raw datasets available in public databases on COVID-19, focusing on the V3-V4 region of the bacterial genome. In total, seven studies were included. All samples underwent the same bioinformatics pipeline, evaluating the differential abundance of these seven bacterial genera at each level of severity. The reanalysis identified significant changes in differential abundance. Bifidobacterium emerged as a potential biomarker of disease severity and a therapeutic target. Bacteroides presented a complex pattern, possibly related to disease-associated inflammation or opportunistic pathogen growth. Lactobacillus showed significant changes in abundance across the COVID-19 stages. On the other hand, Akkermansia and Faecalibacterium did not show significant differences, while Oscillospira and Ruminococcus produced statistically significant results but with limited relevance to COVID-19 severity. Our findings reveal new insights into the differential abundance of key bacterial genera in COVID-19, particularly Bifidobacterium and Bacteroides.

Species traits explaining long-term abundance changes of breeding birds in farmland areas in Álava (N Spain)

In recent decades, the populations of many common bird species have greatly declined in Europe, particularly in farmland habitats. However, this decline has not affected every species, and to understand the mechanisms behind this interspecific variability, its relationship with several species-specific traits has been studied repeatedly. We used this approach to analyse long-term changes in the abundance of breeding passerines in farmland areas in northern Spain. Abundance changes were quantified in 2015 and 2016 by repeating the same line transects conducted in 1988/89 in three agricultural habitats located along a steep Atlantic-Mediterranean gradient in the province of Álava. We found that total bird abundance did not decline, as most species not closely linked to farmland habitats showed positive population changes, while the number of increasing and decreasing farmland specialists was similar. Specific traits explained a substantial proportion of the variability in abundance change, as warm-dwelling species and those occupying habitats with a complex vegetation structure showed more positive changes than those preferring colder conditions and more open habitats. These patterns can be explained by climate warming and by the increase in hedge and forest cover in the study area. Although we did not find a long-term decline in the overall abundance of the studied bird community nor in that of farmland specialists, open habitat species associated with a cool climate should be the focus of particular concern.

Genes involved in carbon, nitrogen, and sulfur cycling in an important estuarine ecosystem show coherent shifts in response to changes in environmental conditions

AbstractWhile metagenomics can provide insight into microbial community metabolic potential, understanding factors that influence gene abundance is necessary to maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa, methodological biases, or issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of key genes for bacterial photosynthesis, nitrogen, and sulfur metabolism with each other and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g., temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting modular pathway structure, methodological errors, or discrepancies in gene copy number between taxonomic groups. To be suitable indicators of biogeochemical processes for models, genes or pathways should be strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process.

Modification of the Sommerfeld effect due to coannihilator decays

Abstract In dark matter coannihilation scenarios, the Sommerfeld effect of coannihilators is usually important in calculations of dark matter thermal relic abundance. Due to decays of coannihilators, two annihilating coannihilators can only approach each other from a finite initial separation. While conventional derivations of Sommerfeld factors essentially assume an infinite initial separation, Sommerfeld factors for a pair of annihilating coannihilators may be different. We find that the Sommerfeld factor for a pair of coannihilators is less prominent than the one obtained without considering decays. The modification of the Sommerfeld factor may result in a change of the dark matter thermal relic abundance well beyond the percent level. Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Article funded by SCOAP3 and published under licence by Chinese Physical Society and the Institute of High Energy Physics of the Chinese Academy of Science and the Institute of Modern Physics of the Chinese Academy of Sciences and IOP Publishing Ltd.

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays

Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed.Key points• The applied methodology was successful to obtain biomass suitable to perform BMP assays.• The microbial community was resilient to external biomass addition.• Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.Graphical