Interactions of long-term grazing and woody encroachment can shift soil biogeochemistry and microbiomes in savanna ecosystems

Semi-arid grasslands and savannas in the southern Great Plains USA are extensively used for livestock grazing. Over the past century, Juniperus (juniper) and Quercus (oak) species abundance have increased due to intensive grazing and reduced fire frequency. We investigated the interactions between livestock grazing history (none, moderate, heavy) and vegetation cover (grassland, juniper, oak) using a ∼ 70-year grazing experiment in west-central Texas. We explored effects on soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), microbial community composition, and function. SOC and TN were 50–150 % higher under juniper and oak compared to grasslands, and 10–30 % lower in grazed vs. ungrazed areas. Vegetation × grazing interaction showed greater SOC and TN loss under oak than juniper or grasslands. Ungrazed controls had higher soil TP than grazed areas, with oak and juniper soils having more TP than grasslands. Bacterial and fungal communities differed between grassland and woody vegetation. Grazing affected only bacterial communities. SOC, TN, TP accounted for differences in community structure. Abundances of genes related to methane, nitrogen, sulfur metabolisms, and dominant fungal trophic modes were linked to soil C, N, P ratios. These findings highlight how long-term livestock grazing and woody plant encroachment influence soil C, N, P cycles, altering soil microbial community structure and function. This study provides insights for savanna ecosystem management and integrating land cover effects into biogeochemical models for global change scenarios

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.

BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades

The Holocene Paleolimnology of Lake Superior

This study describes contributions of glacial meltwater to Lake Superior over the last ~11,000 cal BP (calibrated years before 1950 AD). This research has been motivated by a desire to understand whether glacial meltwater discharge via the Great Lakes into the North Atlantic played a role in Holocene cooling events, such as the Younger Dryas. Rhythmites (interpreted as varves), lithological, mineralogical and grain-size variations, and radiocarbon dating were used to establish chronostratigraphic correlation among four sediment cores from Lake Superior (Duluth, Caribou and Ile Parisienne basins, Thunder Bay Trough). Glacial sediments were deposited between ~10,850 and ~8,800 cal BP. The δ18O values of ostracodes record the presence of glacial meltwater (δ18O of ~ –25 ‰) in ancient Lake Superior as the Laurentide Ice Sheet waxed and waned. Glacial meltwater was increasingly dominant between ~10,850 and ~9,250 cal BP, particularly as thick varves formed in northern portions of the Lake Superior Basin (~10,400-10,200, ~9,900 and ~9,300-9,200 cal BP). Glacial meltwater supply was reduced in the Thunder Bay Trough between ~9,250 and ~8,950 cal BP, but returned from ~8,950 to ~8,800 cal BP. Glacial meltwater flow from the Lake Superior Basin bypassed the Huron Basin several times during this period. Final termination of glacial meltwater supply occurred at ~8,800 cal BP – coincident with cessation of varve formation and inception of ancient Lakes Agassiz-Ojibway and Houghton. Primary productivity was very low and algal growth occurred under conditions of extreme nitrogen deficiency – as determined using TOC, TN and C/N ratios – until glacial meltwater supply to the Basin was ended. The postglacial sediments are non-calcareous. The diatom silica proxy record shows that water δ18O values rapidly increased after glacial meltwater termination, reaching ~ –10 ‰ during the Holocene Thermal Maximum. Water δ18O values decreased at ~3,000 cal BP in response to the Holocene Neoglacial Interval before gradually rising to Lake Superior’s modern value of –8.7 ‰. Aquatic primary productivity, inferred using TOC, TN, and δ13C and δ15N, has increased gradually since ~8,800 cal BP. Primary δD and δ18O values are not preserved by porewater; they instead reflect mixing between ancient and modern lake water

Vegetation change alters soil profile δ15N values at the landscape scale

The assessment of spatial variation in soil δ15N could provide integrative insights on soil N cycling processes across multiple spatial scales. However, little is known about spatial patterns of δ15N within soil profiles in arid and semiarid ecosystems, especially those undergoing vegetation change with a distinct shift in dominance and/or functional type. We quantified how changes from grass to woody plant dominance altered spatial patterns of δ15N throughout a 1.2 m soil profile by collecting 320 spatially-specific soil cores in a 160 m × 100 m subtropical savanna landscape that has undergone encroachment by Prosopis glandulosa (an N2-fixer) during the past century. Leaf δ15N was comparable among different plant life-forms, while fine roots from woody species had significantly lower δ15N than herbaceous species across this landscape. Woody encroachment significantly decreased soil δ15N throughout the entire soil profile, and created horizontal spatial patterns of soil δ15N that strongly resembled the spatial distribution of woody patches and were evident within each depth increment. The lower soil δ15N values that characterized areas beneath woody canopies were mostly due to the encroaching woody species, especially the N2-fixer P. glandulosa, which delivered 15N-depleted organic matter via root turnover throughout the soil profile. Soil δ15N increased with depth, reached maximum values at intermediate depths, and slightly decreased at greater depths. This vertical pattern may be related to the decrease of 15N-depleted organic matter inputs with depth, and to the presence of a subsurface clay-rich argillic horizon at intermediate depths across this landscape, which may favor the accumulation of 15N-enriched residues. These results indicate that succession from grassland to woodland has altered the spatial variation in soil δ15N across the landscape and to considerable depth, suggesting significant changes in the relative rates of N-inputs vs. N-losses in this subtropical system after vegetation change

Arabidopsis UMAMIT24 and 25 are amino acid exporters involved in seed loading

International audiencePhloem-derived amino acids are the major source of nitrogen supplied to developing seeds. Amino acid transfer from the maternal to the filial tissue requires at least one cellular export step from the maternal tissue prior to the import into the symplasmically isolated embryo. Some members of UMAMIT (usually multiple acids move in an out transporter) family (UMAMIT11, 14, 18, 28, and 29) have previously been implicated in this process. Here we show that additional members of the UMAMIT family, UMAMIT24 and UMAMIT25, also function in amino acid transfer in developing seeds. Using a recently published yeast-based assay allowing detection of amino acid secretion, we showed that UMAMIT24 and UMAMIT25 promote export of a broad range of amino acids in yeast. In plants, UMAMIT24 and UMAMIT25 are expressed in distinct tissues within developing seeds; UMAMIT24 is mainly expressed in the chalazal seed coat and localized on the tonoplast, whereas the plasma membrane-localized UMAMIT25 is expressed in endosperm cells. Seed amino acid contents of umamit24 and umamit25 knockout lines were both decreased during embryogenesis compared with the wild type, but recovered in the mature seeds without any deleterious effect on yield. The results suggest that UMAMIT24 and 25 play different roles in amino acid translocation from the maternal to filial tissue; UMAMIT24 could have a role in temporary storage of amino acids in the chalaza, while UMAMIT25 would mediate amino acid export from the endosperm, the last step before amino acids are taken up by the developing embryo

Biochar amendment suppresses N 2 O emissions but has no impact on 15 N site preference in an anaerobic soil

Rationale Biochar amendments often decrease N2O gas production from soil, but the mechanisms and magnitudes are still not well characterized since N2O can be produced via several different microbial pathways. We evaluated the influence of biochar amendment on N2O emissions and N2O isotopic composition, including 15N site preference (SP) under anaerobic conditions. Methods An agricultural soil was incubated with differing levels of biochar. Incubations were conducted under anaerobic conditions for 10 days with and without acetylene, which inhibits N2O reduction to N2. The N2O concentrations were measured every 2 days, the SPs were determined after 5 days of incubation, and the inorganic nitrogen concentrations were measured after the incubation. Results The SP values with acetylene were consistent with N2O production by bacterial denitrification and those without acetylene were consistent with bacterial denitrification that included N2O reduction to N2. There was no effect of biochar on N2O production in the presence of acetylene between day 3 and day 10. However, in the absence of acetylene, soils incubated with 4% biochar produced less N2O than soils with no biochar addition. Different amounts of biochar amendment did not change the SP values. Conclusions Our study used N2O emission rates and SP values to understand biochar amendment mechanisms and demonstrated that biochar amendment reduces N2O emissions by stimulating the last step of denitrification. It also suggested a possible shift in N2O‐reducing microbial taxa in 4% biochar samples

A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans

Extant African great apes and humans are thought to have diverged from each other in the Late Miocene. However, few hominoid fossils are known from Africa during this period. Here we describe a new genus of great ape (Nakalipithecus nakayamai gen. et sp. nov.) recently discovered from the early Late Miocene of Nakali, Kenya. The new genus resembles Ouranopithecus macedoniensis (9.6–8.7 Ma, Greece) in size and some features but retains less specialized characters, such as less inflated cusps and better-developed cingula on cheek teeth, and it was recovered from a slightly older age (9.9–9.8 Ma). Although the affinity of Ouranopithecus to the extant African apes and humans has often been inferred, the former is known only from southeastern Europe. The discovery of N. nakayamai in East Africa, therefore, provides new evidence on the origins of African great apes and humans. N. nakayamai could be close to the last common ancestor of the extant African apes and humans. In addition, the associated primate fauna from Nakali shows that hominoids and other non-cercopithecoid catarrhines retained higher diversity into the early Late Miocene in East Africa than previously recognized

Development of a real-time imaging system for hypoxic cell apoptosis

Hypoxic regions within the tumor form due to imbalances between cell proliferation and angiogenesis; specifically, temporary closure or a reduced flow due to abnormal vasculature. They create environments where cancer cells acquire resistance to therapies. Therefore, the development of therapeutic approaches targeting the hypoxic cells is one of the most crucial challenges for cancer regression. Screening potential candidates for effective diagnostic modalities even under a hypoxic environment would be an important first step. In this study, we describe the development of a real-time imaging system to monitor hypoxic cell apoptosis for such screening. The imaging system is composed of a cyclic luciferase (luc) gene under the control of an improved hypoxic-responsive promoter. The cyclic luc gene product works as a caspase-3 (cas-3) monitor as it gains luc activity in response to cas-3 activation. The promoter composed of six hypoxic responsible elements and the CMV IE1 core promoter drives the effective expression of the cyclic luc gene in hypoxic conditions, enhancing hypoxic cell apoptosis visualization. We also confirmed real-time imaging of hypoxic cell apoptosis in the spheroid, which shares properties with the tumor. Thus, this constructed system could be a powerful tool for the development of effective anticancer diagnostic modalities

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.

BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades