Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations.

The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and ß-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.

Endmember extraction and abundance estimation algorithm based on double-compressed sampling.

Based on double-compressed sampling, a hyperspectral spectral unmixing algorithm (SU_DCS) is proposed, which could directly complete the endmember extraction and abundance estimation. On the basis of the linear mixed model (LMM), we designed spatial and spectral sampling matrices, obtained spatial and spectral measurement data, and constructed a joint unmixing model containing endmember and abundance information. By using operator separation and Lagrangian multiplier algorithm, the endmember matrix, abundance matrix and remixing image can be quickly obtained by matrix operation. The parameters of the unmixing algorithm, including regularization parameter, convergence threshold and spatial sampling rate, are determined using synthetic simulated hyperspectral data. The proposed algorithm is applied to two kinds of real hyperspectral data, with or without ground truth, in order to verify the effectiveness and reliability of the algorithm. Firstly, we provide the performance of the algorithm on real datasets without ground truth. Compared with algorithm VCA_FCLS and algorithm CPPCA_VCA_FCLS, the endmember spectral curve extracted by the proposed SU_DCS is almost consistent with that obtained by VCA_FCLS, and is more smooth than that of obtained by CPPCA_VCA_FCLS. Additionally, the abundance estimation map estimated by the SU_DCS has consistency with the results obtained by VCA_FCLS. Moreover, the proposed SU_DCS has higher peak signal-to-noise ratio (PSNR) for remixing images with higher computational efficiency. Secondly, we provide the performance of the proposed algorithm on four real datasets with ground truth, including dataset Cuprite, dataset Samson, dataset Jasper and dataset Urban. We provide the results of endmember extraction and abundance estimation from the compressed data under different sampling rate conditions. The extracted endmember maintains good consistency with the true spectral curves, and the estimated abundance map can also maintain good spatial consistency with the ground truth. The comparison results with other four comparative algorithms also indicate that the proposed algorithm can obtain relatively accurate endmembers and abundance information from compressed data, the reliability and validity of the proposed algorithm have been proved. In summary, the main innovation of the proposed algorithm is that it can extract endmembers and estimate abundance with high accuracy from a small amount of measurement data.

Persistence and pathway of glyphosate degradation in the coastal wetland soil of central Delaware.

Glyphosate is a globally dominant herbicide. Here, we studied the degradation and microbial response to glyphosate application in a wetland soil in central Delaware for controlling invasive species (Phragmites australis). We applied a two-step solid-phase extraction method using molecularly imprinted polymers designed for the separation and enrichment of glyphosate and aminomethylphosphonic acid (AMPA) from soils before their analysis by ultra-high-performance liquid chromatography (UHPLC) and Q Exactive Orbitrap mass spectrometry methods. Our results showed that approximately 90 % of glyphosate degraded over 100 d after application, with AMPA being a minor (<10 %) product. Analysis of glyphosate-specific microbial genes to identify microbial response and function revealed that the expression of the phnJ gene, which codes C-P lyase enzyme, was consistently dominant over the gox gene, which codes glyphosate oxidoreductase enzyme, after glyphosate application. Both gene and concentration data independently suggested that C-P bond cleavage-which forms sarcosine or glycine-was the dominant degradation pathway. This is significant because AMPA, a more toxic product, is reported to be the preferred pathway of glyphosate degradation in other soil and natural environments. The degradation through a safer pathway is encouraging for minimizing the detrimental impacts of glyphosate on the environment.

A trawl collected dataset of Johnius (Actinopterygii, Sciaenidae) species in central-western Taiwanese waters.

Background: Sciaenidae is one of the most important coastal fisheries in Taiwan, both in production and economic value. It is also significant as the main targetted diet of Chinese white dolphins, Sousachinensis, especially for the genus Johnius, such as J.taiwanensis, J.belangerii and J.distinctus, which is primarily found in central-western Taiwan coastal waters. Despite an abundance of Johnius species occurrences reported in the Global Biodiversity Information Facility (GBIF) and the Taiwan Biodiversity Information Facility (TaiBIF) data portals (Mozambique, Australia, Taiwan, Korea, India, Indonesia, South Africa, Pakistan, Vietnam and China), there are no specific datasets that properly document the regional distribution of this genus, especially in Taiwanese waters. Thus, this paper describes a dataset of genus Johnius occurrences in waters on the central-western coast of Taiwan. The data collection for the present study was conducted from 2009 until 2020 and comprised 62 sampling events and 133 occurrence records. All fish specimens were collected by trawling in Miaoli, Changhwa and Yunlin Counties, Taiwan and brought back to the lab for identification, individual number count and body weight measurement. These processing data have been integrated and established in the Taiwan Fish Database and published in GBIF. This dataset contains six Johnius species and 2,566 specimens, making it comprehensive Johnius fish fauna and spatial distributional data on the coastal habitat in central-western Taiwanese waters. New information: This dataset contains 133 occurrence records of Johnius species (Sciaenidae) with 2,566 specimens, making it the most extensive public dataset of Johnius distribution records in Taiwan. The publication of this dataset through the TaiBIF and GBIF dataset platforms demonstrated that the number of Johnius spatial and temporal records in Taiwan waters is influenced by the topographical structure of the Changyun Rise (CYR) in combination with the cold current of the China Coastal currents and bound with the warm currents of the Kuroshio and the South China Sea on the central-western coast of Taiwan. The data serve as the foundation for understanding the biogeography and Johnius species ecology in Taiwan's coastal waters, which present a 2°C water temperature difference split at the CYR.

Diversity and ecological niche model of malaria vector and non-vector mosquito species in Covè, Ouinhi, and Zangnanado, Southern Benin.

The present study aimed to assess mosquito species diversity, distribution, and ecological preferences in the Covè, Ouinhi, and Zangnanado communes, Southern Benin. Such information is critical to understand mosquito bio-ecology and to focus control efforts in high-risk areas for vector-borne diseases. Mosquito collections occurred quarterly in 60 clusters between June 2020 and April 2021, using human landing catches. In addition to the seasonal mosquito abundance, Shannon's diversity, Simpson, and Pielou's equitability indices were also evaluated to assess mosquito diversity. Ecological niche models were developed with MaxEnt using environmental variables to assess species distribution. Overall, mosquito density was higher in the wet season than in the dry season in all communes. A significantly higher Shannon's diversity index was also observed in the wet season than in the dry seasons in all communes (p < 0.05). Habitat suitability of An. gambiae s.s., An. coluzzii, Cx. quinquefasciatus and Ma. africana was highly influenced by slope, isothermality, site aspect, elevation, and precipitation seasonality in both wet and dry seasons. Overall, depending on the season, the ecological preferences of the four main mosquito species were variable across study communes. This emphasizes the impact of environmental conditions on mosquito species distribution. Moreover, mosquito populations were found to be more diverse in the wet season compared to the dry season.

Distribution and effects of microplastics as carriers of heavy metals in river surface sediments.

There are few studies on microplastics (MPs) in urban river sediments compared to oceans, soils, and even rivers. In this study, the seasonal abundance of MPs, as well as their influencing factors on heavy metal adsorption in river sediments of the Ancient Canal of Zhenjiang City, China, were investigated for the first time. Through on-site sampling, microscopic observation, Raman spectroscopy, scanning electron microscopy, and high-temperature digestion, the abundance, shape, color, particle size, type, and surface characteristics of MPs in Ancient Canal sediments in different seasons, as well as the influencing factors of MPs as heavy metal carriers in different seasons, were analyzed. The results showed that the average abundance of MPs is 2049.09 ± 883.78 and 2216.36 ± 826.21 items kg-1 dry sediments in summer and winter, respectively, and different sites change significantly. In addition, particle sizes, types, colors, and shapes of MPs exhibited seasonal variations. Four MPs shapes were mainly observed: fibers, fragments, particles, and films. Among them, MPs in summer sediments are mainly fiber, and MPs in winter sediments are mainly particles. In the sediment in summer and winter, transparent MPs and small-size (<0.5 mm) MPs are the main ones, where the abundance of MPs decreased with increasing MPs size. The main MPs species are polyvinyl chloride (PVC), polystyrene (PS), polypropylene (PP), polyethylene terephthalate (PET), polycarbonate (PC), and polyethylene (PE), with PP being the predominant MPs in the sediments in different seasons. Scanning electron microscopy-energy dispersive spectrometer (SEM-EDS) revealed that the surfaces of the MPs were characterized by rough, porous, cracked, and torn, with the attachment of various heavy metal elements, and all of the heavy metal elements accumulated to different degrees on the MPs. There was a significant positive correlation (p < 0.05) between the Mn content in the MPs and the Mn content in the sediments in winter, suggesting that the Mn in the MPs in winter may be derived from the sediments. In addition, the type, shape, size, and color of MPs affect the adsorption capacity of heavy metals. Most of the adsorption of MPs on Pb showed a significant negative correlation, and the adsorption of MPs on Cr, Zn, Cu, Cd, and Mn showed a significant positive correlation. MPs can be used as carriers of heavy metals, which will further enhance the hazards of living organisms and pose a potential threat to the safety of the urban river environment.

Highly accurate measurement of the relative abundance of oral pathogenic bacteria using colony-forming unit-based qPCR.

PURPOSE: Quantitative polymerase chain reaction (qPCR) has recently been employed to measure the number of bacterial cells by quantifying their DNA fragments. However, this method can yield inaccurate bacterial cell counts because the number of DNA fragments varies among different bacterial species. To resolve this issue, we developed a novel optimized qPCR method to quantify bacterial colony-forming units (CFUs), thereby ensuring a highly accurate count of bacterial cells. METHODS: To establish a new qPCR method for quantifying 6 oral bacteria namely, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Fusobacterium nucleatum, and Streptococcus mutans, the most appropriate primer-probe sets were selected based on sensitivity and specificity. To optimize the qPCR for predicting bacterial CFUs, standard curves were produced by plotting bacterial CFU against Ct values. To validate the accuracy of the predicted CFU values, a spiking study was conducted to calculate the recovery rates of the predicted CFUs to the true CFUs. To evaluate the reliability of the predicted CFU values, the consistency between the optimized qPCR method and shotgun metagenome sequencing (SMS) was assessed by comparing the relative abundance of the bacterial composition. RESULTS: For each bacterium, the selected primer-probe set amplified serial-diluted standard templates indicative of bacterial CFUs. The resultant Ct values and the corresponding bacterial CFU values were used to construct a standard curve, the linearity of which was determined by a coefficient of determination (r²) >0.99. The accuracy of the predicted CFU values was validated by recovery rates ranging from 95.1% to 106.8%. The reliability of the predicted CFUs was reflected by the consistency between the optimized qPCR and SMS, as demonstrated by a Spearman rank correlation coefficient (ρ) value of 1 for all 6 bacteria. CONCLUSIONS: The CFU-based qPCR quantification method provides highly accurate and reliable quantitation of oral pathogenic bacteria.

Mealybug Population Dynamics: A Comparative Analysis of Sampling Methods for Saccharicoccus sacchari and Heliococcus summervillei in Sugarcane (Saccharum sp. Hybrids).

This research is focused on a comparative field-based study of the population dynamics and sampling methods of two mealybug species, Saccharicoccus sacchari (Cockerell, 1895) (Hemiptera: Coccomorpha, Pseudococcidae) and Heliococcus summervillei (Brookes, 1978) (Hemiptera: Coccomorpha, Pseudococcidae), in sugarcane (Saccharum sp. hybrids) (f. Poaceae) over consecutive growing seasons. The research monitored and compared the above- and belowground populations and seasonal abundance of these two mealybug species in sugarcane fields in Far North Queensland, with non-destructive sampling techniques of yellow sticky traps, pan traps, and stem traps, and destructive sampling of the whole leaf and whole plant. The results indicated that S. sacchari (n = 29,137) was more abundant and detected throughout the growing season, with population peaks in the mid-season, while H. summervillei (n = 2706) showed peaks of the early-season activity. S. sacchari is primarily located on sugarcane stems and roots, compared to H. summervillei, which is located on leaves and roots. The whole-leaf collection and stem trap were the most effective sampling techniques for quantification of H. summervillei and S. sacchari, respectively. This study enhanced the understanding of S. sacchari and the first-ever record of H. summervillei on sugarcane in Australia and will contribute to the development of more effective pest management strategies.

Feeding Preferences of the Bean Leaf Beetle (Ootheca spp.) (Coleoptera: Chrysomelidae): Insights for Targeted Pest Control Strategies in Uganda.

The bean leaf beetle (BLB) (Ootheca spp.) is a polyphagous pest causing significant yield losses in Uganda, particularly in the Northern and Eastern regions on various hosts plants. Despite its polyphagous behaviour, the BLB exhibits preferential feeding, offering an opportunity for targeted pest management. This study explored its feeding preferences across seven crops: common bean, cowpea, greengram, okra, roselle (malakwang), groundnuts, and soybean. This study was conducted in Arua and Lira districts using a randomized complete block design for two rainy seasons (2018A and 2018B). The results showed significant differences in BLB abundance and foliar damage among host crops, locations, days after planting and seasons. Cowpea was the most preferred crop while groundnuts was the least preferred. Therefore, cowpea can be recommended for use as a trap for managing Ootheca spp. in gardens where it is not the main crop. There was a higher pest abundance in Arua than in Lira. There was also a higher pest abundance in 2018A than in 2018B. These findings highlight the importance of understanding BLB's feeding preferences for implementing effective IPM strategies, emphasizing the potential role of trap cropping, especially with cowpea, to minimize BLB damage in resource-constrained agricultural settings.

Refocusing the microbial rare biosphere concept through a functional lens.

The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.

Population size and structure of beisa oryx and gerenuk in Geralle National Park, southeastern Ethiopia.

The study was conducted to determine the population size of endangered Oryx beisa (Rüppell, 1835), and near-threatened Litocranius walleri (Brooke, 1878) of uncertain global population estimates in Geralle National Park, southeastern Ethiopia. Systematic line transects were established with a transect length range of 2.3 to 6.8 km long (a total of 165.4 km long with a sighting distance of 150 m after truncation). The combination of AIC and chi-square p-values was used as model selection criteria for density/population size estimation in distance sampling software. The lowest AIC, ∆AIC (close to zero), and Chi-square tests (p-value > .05) were selected with adequate model fit. The minimum observation was 67 individuals of beisa oryx in the dry season. The maximum observation was 349 individuals of gerenuk during the wet season. The minimum detection probability of oryx was in the wet season (p â = 76 ± 26), and the minimum detection probability of gerenuk was (p â = 75 ± 1) in both seasons. The two-season pooled density analyzed for studied species indicated (0.85 ± 0.34, 1.24 ± 0.47, beisa oryx/km2), and (3.82 ± 0.6, 4.88 ± 0.7 gerenuk/km2) in dry and wet seasons, respectively. It can be concluded from the results of the study that GNP is home to previously undiscovered healthy populations of the endangered beisa oryx and near-threatened gerenuk. So it is recommended to undergo in-depth population studies, including other species available in the national park and their habitat components, so as to design sound, sustainable conservation measures for the wildlife resources in the area.

A Chemoproteomic Approach to Monitor Native Iron-Sulfur Cluster Binding.

Iron-sulfur (Fe-S) clusters are essential redox-active metallocofactors participating in electron transfer, radical chemistry, primary metabolism, and gene regulation. Successful trafficking and incorporation of Fe-S clusters into target proteins are critical to proper cellular function. While biophysical studies of isolated Fe-S proteins provide insight into the structure and function of these inorganic cofactors, few strategies currently exist to directly interrogate Fe-S cluster binding within a cellular environment. Here, we describe a chemoproteomic platform to report on Fe-S cluster incorporation and occupancy directly within a native proteome, enabling the characterization of Fe-S biogenesis pathways and the identification of undiscovered Fe-S proteins.

Comprehensive risk assessment of microplastics in tidal channel sediments in amazonian mangroves (northern Brazil).

Pollution by microplastics (MPs) in mangroves is a growing concern, given its potential ecological and human health impacts. The characteristics of microplastic pollution and a risk assessment of MPs in the Amazon region's coastal sediments are still insufficient, and information about MP pollution in the benthic component of the mangrove ecosystem is lacking. We analyzed MP concentrations in the surface sediment of 9 stations in three tidal channels along the Ajuruteua Peninsula connected to the Caeté River estuary, aiming to assess the hazard level on the environment based on the Pollution Load Index (PLI). Raman and Fourier transform infrared spectroscopy determined the MP's chemical composition. The results showed that the abundance of sediment MPs ranged from 100 to 1200 items kg-1, with an average of 433 ± 261.6 items kg-1. The MPs were mainly composed of transparent and blue fragments and fibers, ranging in size from 100 to 5000 µm. Six types of polymers were identified, including alkyd varnish (AV), resin dispersion (RD), chlorinated polyethylene (CPE), polyethylene-polypropylene (PE-PP), low-density polyethylene (LDPE), and hostaperm blue (HB). Hydrodynamic processes within estuaries and tidal channels play a crucial role in explaining the concentrations found, as circulation determines the pattern of sediment deposition and the particles adhered to it. PLI risk assessment showed that all sampling sites were at hazard level I: a low level of contamination in the mangrove sediments. However, a more comprehensive and systematic monitoring campaign is needed to expand our knowledge about pollution and contamination by MPs in Amazon mangrove areas.

Species Diversity of Anastrepha Fruit Flies (Diptera: Tephritidae) in Environments with Different Levels of Anthropogenic Changes.

Studies on the diversity of Anastrepha species have been conducted mainly in agricultural orchards due to the economic importance of this insect group, consequently, research on fruit flies in undisturbed environments is scarce. Moreover, very few studies have investigated the diversity of fruit flies in urban areas, where fruit flies survive under native or exotic hosts. Thus, to understand the diversity of Anastrepha species in an environment with different anthropization degrees, surveys were carried out in four areas of the "Luiz de Queiroz" campus, in Piracicaba, São Paulo State (Brazil), using Multilure traps with putrescine and ammonium acetate for 12 months. The software R 3.6.3 was used to characterize the fruit fly community and the faunistic analysis was carried out using the ANAFAU program. The analysis of species richness and total abundance of fruit flies among the sites was carried out using the rarefaction method and adjustment to the generalized linear model (GLM) using the Poisson distribution, respectively. We collected 1,080 females and 14 species of Anastrepha in the four sampled sites. Anastrepha fraterculus and A. obliqua were the predominant species (behavioral patterns). Similar to agricultural sites, A. fraterculus and A. obliqua also show a predominant occurrence in urban environments.

Not all soil carbon is created equal: Labile and stable pools under nitrogen input.

Anthropogenic activities have raised nitrogen (N) input worldwide with profound implications for soil carbon (C) cycling in ecosystems. The specific impacts of N input on soil organic matter (SOM) pools differing in microbial availability remain debatable. For the first time, we used a much-improved approach by effectively combining the 13C natural abundance in SOM with 21 years of C3-C4 vegetation conversion and long-term incubation. This allows to distinguish the impact of N input on SOM pools with various turnover times. We found that N input reduced the mineralization of all SOM pools, with labile pools having greater sensitivity to N than stable ones. The suppression in SOM mineralization was notably higher in the very labile pool (18%-52%) than the labile and stable (11%-47%) and the very stable pool (3%-21%) compared to that in the unfertilized control soil. The very labile C pool made a strong contribution (up to 60%) to total CO2 release and also contributed to 74%-96% of suppressed CO2 with N input. This suppression of SOM mineralization by N was initially attributed to the decreased microbial biomass and soil functions. Over the long-term, the shift in bacterial community toward Proteobacteria and reduction in functional genes for labile C degradation were the primary drivers. In conclusion, the higher the availability of the SOM pools, the stronger the suppression of their mineralization by N input. Labile SOM pools are highly sensitive to N availability and may hold a greater potential for C sequestration under N input at global scale.

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke.

Although knowledge of the role of the oral microbiome in ischemic stroke is steadily increasing, little is known about the multikingdom microbiota interactions and their consequences. We enrolled participants from a prospective multicentre case-control study and investigated multikingdom microbiome differences using saliva metagenomic datasets (n = 308) from young patients diagnosed with cryptogenic ischemic stroke (CIS) and age- and sex-matched stroke-free controls. Differentially abundant taxa were identified using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC2). Functional potential was inferred using HUMANn3. Our findings revealed significant differences in the composition and functional capacity of the oral microbiota associated with CIS. We identified 51 microbial species, including 47 bacterial, 3 viral, and one fungal species associated with CIS in the adjusted model. Co-abundance network analysis highlighted a more intricate microbial network in CIS patients, indicating potential interactions and co-occurrence patterns among microbial species across kingdoms. The results of our metagenomic analysis reflect the complexity of the oral microbiome, with high diversity and multikingdom interactions, which may play a role in health and disease.

Analysis of Microbiome Data.

The microbiome represents a hidden world of tiny organisms populating not only our surroundings but also our own bodies. By enabling comprehensive profiling of these invisible creatures, modern genomic sequencing tools have given us an unprecedented ability to characterize these populations and uncover their outsize impact on our environment and health. Statistical analysis of microbiome data is critical to infer patterns from the observed abundances. The application and development of analytical methods in this area require careful consideration of the unique aspects of microbiome profiles. We begin this review with a brief overview of microbiome data collection and processing and describe the resulting data structure. We then provide an overview of statistical methods for key tasks in microbiome data analysis, including data visualization, comparison of microbial abundance across groups, regression modeling, and network inference. We conclude with a discussion and highlight interesting future directions.

Inhibition of microbially mediated total organic carbon decomposition in different types of cadmium contaminated soils with wheat straw addition.

Wheat straw returning is a common agronomic measure in the farmland. Understanding organic carbon transformation is of great significance for carbon budget under the premise of widespread distribution of cadmium (Cd) contaminated soils. An incubation experiment was conducted to assess the influence of Cd contamination on the decomposition and accumulation of total organic carbon (TOC) as well as the composition and abundance of bacterial communities in eight soil types with wheat straw addition. The results showed that inhibition of Cd contamination on microbially mediated organic carbon decomposition was affected by soil types. The lower cumulative C mineralization and higher TOC content could be observed in the acidic soils relative to that in the alkaline soils. The content of Cd in soil exhibits different effects on the inhibition in decomposition of TOC. The high dosage level of Cd had stronger inhibitory impact due to its high toxicity. The decomposition of TOC was restricted by a reduction in soil bacterial abundance and weakening of bacterial activities. Redundancy analysis (RDA) indicated that Proteobacteria and Gemmatimonadetes were abundant in alkaline Cd-contaminated soils with wheat straw addition, while Bacteroidetes dominated cumulative C mineralization in acidic Cd-contamination soils. Moreover, the abundance of predicted functional bacteria indicated that high-dose Cd-contamination and acid environment all inhibited the decomposition of TOC. The present study suggested that pH played an important role on carbon dynamics in the Cd-contaminated soils with wheat straw addition.

Consistencies in the dietary and isotopic niche of spotted seatrout, Cynoscion nebulosus, across a salinity gradient within a coastal Louisiana estuary.

Estuaries are essential habitats for recreational and commercial fish that are shaped by both natural and anthropogenic processes. In Louisiana a combination of climate change and planned coastal restoration actions is predicted to increase freshwater introduction to coastal estuaries. As such there is a need to quantify the relationships between estuarine fish ecology and salinity to aid in predicting how species will respond to shifts in salinity. We investigated the relative abundance and dietary niches of adult (24.5 ± 5.4 cm standard length) spotted seatrout Cynoscion nebulosus across varying salinity regimes (oligohaline, mesohaline, and polyhaline) within Barataria Bay, Louisiana, using a combination of net sampling and gut content and stable isotopes analysis. We found that the relative abundance of C. nebulosus was lowest at the oligohaline site, translating to approximately five fewer fish captured for every single psu decrease in a site's average annual salinity. In contrast, we found that diets and, to a lesser extent, isotopic niches had a high degree of overlap across sites with differing salinity regimes. Fish and penaeid shrimp were the most common and important prey taxa recovered from guts at all sites. The small isotopic differences found among sites were likely due to spatial variation in hydrogeochemical baselines, and the observed isotopic overlap provides support for the idea that C. nebulosus move between adjacent salinity regimes and forage throughout Barataria Bay. Our results contribute to a greater understanding of the salinity preference and trophic ecology of C. nebulosus that can aid in predicting their responses to future salinity and habitat changes within Barataria Bay associated with predicted climate change and planned coastal restoration actions.

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China.

BACKGROUND: Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood. RESULTS: In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling. CONCLUSIONS: These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.