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Understanding the dynamics of rhizosphere microbial communities is essential for predicting future ecosystem function, yet most research focuses on either spatial or temporal processes, ignoring combined spatio-temporal effects. Using pyrosequencing, we examined the spatio-temporal dynamics of a functionally important community of rhizosphere microbes, the arbuscular mycorrhizal (AM) fungi. We sampled AM fungi from plant roots growing in a temperate grassland in a spatially explicit manner throughout a year. Ordination analysis of the AM fungal assemblages revealed significant temporal changes in composition and structure. Alpha and beta diversity tended to be negatively correlated with the climate variables temperature and sunshine hours. Higher alpha diversity during colder periods probably reflects more even competitive interactions among AM fungal species under limited carbon availability, a conclusion supported by analysis of beta diversity which highlights how resource limitation may change localized spatial dynamics. Results reveal distinct AM fungal assemblages in winter and summer at this grassland site. A seasonally changing supply of host-plant carbon, reflecting changes in temperature and sunshine hours, may be the driving force in regulating the temporal dynamics of AM fungal communities. Climate change effects on seasonal temperatures may therefore substantially alter future AM fungal community dynamics and ecosystem functioning.

The dust emission polarization spectrum—how the polarization percentage changes with wavelength—serves as a probe of dust grain properties in star-forming regions. In this paper, we present 89–214 μm polarization spectrum measurements obtained from SOFIA/HAWC+ for three star-forming clouds: OMC1, M17, and W3. We find that all three clouds have an overall decreasing polarization percentage with increasing wavelength (i.e., a “falling polarization spectrum”). We use SOFIA and Herschel data to create column density and temperature maps for each cloud. We fit for the slope of the polarization spectrum at each sky position in each cloud, and using the Pearson r coefficient, we probe each cloud for possible correlations of slope with column density and slope with temperature. We also create plots of slope versus column density and slope versus temperature for each cloud. For the case of OMC1, our results are consistent with those presented by J. Michail et al., who carried out a similar analysis for that cloud. Our plots of polarization spectrum slope versus column density reveal that for each cloud there exists a critical column density below which a falling polarization spectrum is not observed. For these more diffuse sight lines, the polarization spectrum is instead flat or slightly rising. This finding is consistent with a hypothesis presented 25 yr ago in a paper led by R. Hildebrand based on Kuiper Airborne Observatory data. This hypothesis is that regions shielded from near-IR radiation are required to produce a sharply falling polarization spectrum.

Protein sequences preserved in two Quaternary taxa, Macrauchenia and Toxodon , resolve the evolutionary history of South American native ungulates. South American ungulates demystified When Charles Darwin first unearthed the remains of the South American native ungulates — herbivorous mammals that evolved in isolation on the South American continent for tens of millions of years — he declared them “the strangest animals ever discovered”. Their origins are obscured by rampant convergence of morphology, and work with ancient DNA has been similarly frustrating. Ian Barnes and colleagues have circumvented these problems by screening protein sequences preserved in two Quaternary taxa, Macrauchenia and Toxodon , to show that their closest relatives among other mammals are the Perissodactyls (odd-toed ungulates such as horses and rhinos) rather than among the Afrotheres (elephants, sirenians and allies). No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as ‘South American native ungulates’. To Charles Darwin 1 , 2 , who first collected their remains, they included perhaps the ‘strangest animal[s] ever discovered’. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago 3 , or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria 4 , 5 , 6 . Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies 7 , 8 , 9 . Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed 5 , 6 , but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates 4 , 6 from ‘condylarths’, a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.

The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. The sequence annotation accuracies of metagenomic analysis tools were evaluated using a simulated metagenome. Graphical Abstract Figure. The sequence annotation accuracies of metagenomic analysis tools were evaluated using a simulated metagenome.

Less than half of anthropogenic carbon dioxide emissions remain in the atmosphere. While carbon balance models imply large carbon uptake in tropical forests, direct on-the-ground observations are still lacking in Southeast Asia. Here, using long-term plot monitoring records of up to half a century, we find that intact forests in Borneo gained 0.43 Mg C ha −1 per year (95% CI 0.14–0.72, mean period 1988–2010) in above-ground live biomass carbon. These results closely match those from African and Amazonian plot networks, suggesting that the world’s remaining intact tropical forests are now en masse out-of-equilibrium. Although both pan-tropical and long-term, the sink in remaining intact forests appears vulnerable to climate and land use changes. Across Borneo the 1997–1998 El Niño drought temporarily halted the carbon sink by increasing tree mortality, while fragmentation persistently offset the sink and turned many edge-affected forests into a carbon source to the atmosphere. The existence of a pan-tropical forest carbon sink remains uncertain due to the lack of data from Asia. Here, using direct on-the-ground observations, the authors confirm remaining intact forests in Borneo have provided a long-term carbon sink, but carbon net gains are vulnerable to drought and edge effects.

Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

The response of tropical forests to global climate variability and change remains poorly understood. Results from long-term studies of permanent forest plots have reported different, and in some cases opposing trends in tropical forest dynamics. In this study, we examined changes in tree growth rates at four long-term permanent tropical forest research plots in relation to variation in solar radiation, temperature and precipitation. Temporal variation in the stand-level growth rates measured at five-year intervals was found to be positively correlated with variation in incoming solar radiation and negatively related to temporal variation in night-time temperatures. Taken alone, neither solar radiation variability nor the effects of night-time temperatures can account for the observed temporal variation in tree growth rates across sites, but when considered together, these two climate variables account for most of the observed temporal variability in tree growth rates. Further analysis indicates that the stand-level response is primarily driven by the responses of smaller-sized trees (less than 20 cm in diameter). The combined temperature and radiation responses identified in this study provide a potential explanation for the conflicting patterns in tree growth rates found in previous studies.

The polarization spectrum, or wavelength dependence of the polarization fraction, of interstellar dust emission provides important insights into the grain alignment mechanism of interstellar dust grains. We investigate the far-infrared polarization spectrum of a realistic simulated high-mass star-forming cloud under various models of grain alignment and emission. We find that neither a homogeneous grain alignment model nor a grain alignment model that includes collisional dealignment is able to produce the falling spectrum seen in observations. On the other hand, we find that a grain alignment model with grain alignment efficiency dependent on local temperature is capable of producing a falling spectrum that is in qualitative agreement with observations of OMC-1. For the model most in agreement with OMC-1, we find no correlation between the temperature and the slope of the polarization spectrum. However, we do find a positive correlation between the column density and the slope of the polarization spectrum. We suggest this latter correlation to be the result of wavelength-dependent polarization by absorption.