Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Biological nitrogen fixation contributes to the pool of plant-available N in both bulk soil and the rhizosphere. Here we investigated the co-association and assemblage process of diazotrophic community members in both rhizosphere and bulk soil of wheat fields. The diazotrophic community structure in the rhizosphere was significantly different and comprised a less competitive and more stable network structure when compared with that of the bulk soil. Deterministic versus stochastic community assemblage processes were quantified using betaNTI scores, demonstrating that deterministic processes decreased in importance with distance from plant roots. Soil pH was correlated with diazotrophic community structure and diversity, and community structure showed greater connectivity and stability in soils with neutral pH relative to those in acidic or alkaline soils. Stochastic processes dominated the assemblage of the diazotrophic community in soils with neutral pH, while deterministic processes dominated in acidic or alkaline soils. These results suggest that soil pH may play an essential role in the interaction and assemblage processes of the diazotrophic community in the rhizosphere and bulk soils, which could enhance our understanding of biological nitrogen fixation in agricultural soils.

Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields

Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.

Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils.

Minimal tillage management of extensive crops like wheat can provide significant environmental services but can also lead to adverse interactions between soil borne microbes and the host. Little is known about the ability of the wheat cultivar to alter the microbial community from a long-term recruitment standpoint, and whether this recruitment is consistent across field sites. To address this, nine winter wheat cultivars were grown for two consecutive seasons on the same plots on two different farm sites and assessed for their ability to alter the rhizosphere bacterial communities in a minimal tillage system. Using deep amplicon sequencing of the V1-V3 region of the 16S rDNA, a total of 26,604 operational taxonomic units (OTUs) were found across these two sites. A core bacteriome consisting of 962 OTUs were found to exist in 95% of the wheat rhizosphere samples. Differences in the relative abundances for these wheat cultivars were observed. Of these differences, 24 of the OTUs were found to be significantly different by wheat cultivar and these differences occurred at both locations. Several of the cultivar-associated OTUs were found to correspond with strains that may provide beneficial services to the host plant. Network correlations demonstrated significant co-occurrences for different taxa and their respective OTUs, and in some cases, these interactions were determined by the wheat cultivar. Microbial abundances did not play a role in the number of correlations, and the majority of the co-occurrences were shown to be positively associated. PICRUSt was used to determine potential functions associated with OTUs by association with rhizosphere members which have sequenced metagenomics data. Potentially-beneficial pathways for nitrogen, sulfur, phosphorus, and malate metabolism, as well as antimicrobial compounds, were inferred from this analysis. Differences in these pathways and their associated functions were found to differ by wheat cultivar. In conclusion, our study suggests wheat cultivars are involved in shaping the rhizosphere by differentially altering the bacterial OTUs consistently across different sites, and these altered bacterial communities may provide beneficial services to the host.

/pdf/community-structure-species-variation-and-potential-2p6rtvalbv.pdf

Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat ( Triticum aestivum ) Cultivars.

The biological nitrogen input is essential for nutrient enrichment in natural grassland ecosystems. This process is carried out by diazotrophic microbes. However, the patterns and assembly processes of diazotrophic communities in grassland soil are not fully understood, especially in alpine meadows of high-altitude Qinghai-Tibet Plateau (QTP). In this study, the diversity patterns and community assembly processes of soil diazotrophic communities were investigated in QTP alpine meadows. The results showed that different diazotrophic taxa responded differentially to the increase of soil pH, and α-diversity increased linearly with pH values. Diazotrophic community turnover was enhanced by the increased variation in soil pH, moreover, it also showed strong response to mean annual temperature. Null model analysis showed that deterministic processes were most important in shaping the phylogenetic community structure and assembly of diazotrophs. Diazotrophic communities of each sampling site tended to be phylogenetically clustered, while communities at high pH soils (pH 7.00 to 8.00) showed more clustering than those of low pH (pH 5.02 to 7.00). The soil pH is a main driver in structuring soil diazotrophic community assembly by regulating the relative importance of deterministic and stochastic processes in QTP alpine meadows.

Soil pH is a major driver of soil diazotrophic community assembly in Qinghai-Tibet alpine meadows

Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.

/pdf/the-diversity-and-co-occurrence-patterns-of-n2-fixing-4xfu1z0brv.pdf

Liyou Wu

Papers

The Diversity and Co-occurrence Patterns of N2-Fixing Communities in a CO2-Enriched Grassland Ecosystem