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

B6nassy, C., 1955. R6marques sur deux Aphelinid6s: Aphelinus mytilaspidis Le Baron et Aphytis proclia Walker. Annls l~piphyt. 6: 11-17. Lord, F. T. & MacPhee, A. W., 1953. The influence of spray programs on the fauna of apple orchards in Nova Scotia II. Oyster shell scale. Can. Ent. 79: 196-209. Pickett, A. D., 1946. A progress report on long term spray programs. Rep. Nova Scotia Fruit Grow. Ass. 83 : 27-31. Pickett, A. D., 1967. The influence of spray programs on the fauna of apple orchards in Nova Scotia XIV. Can. Ent. 97: 816-821. Tothill, J. D., 1918. The predacious mite Hemisarcoptes malus Shimer and its relation to the natural control of the oyster shell scale Lepidosaphes ulmi L. Agric. Gaz. Can. 5 : 234-239.

http://link.springer.com/content/pdf/10.1007/BF01976688.pdf

Soil enzymes: Kuprevich, V. F. & Shcherbakova, T. A.: Translated from the Russian edition (1966), published by the Indian National Scientific Documentation Centre, New Delhi 1971. 392 pp., offset printing from type script, paper cover. Obtainable from U.S. Department of Commerce, National Technical Information Service, Springfield, Va. 22151

The soil volume affected by roots – the rhizosphere – is one of the most important microbial hotspots determining the processes, dynamics and cycling of carbon (C), nutrients and water in terrestrial ecosystems. Rhizosphere visualization is necessary to understand, localize and quantify the ongoing processes and functions, but quantitative conclusions are very uncertain because of: 1) the continuum of the parameters between the root surface and root-free soil, i.e., there are no sharp borders, 2) differences in the distributions of various parameters (C, nutrients, pH, enzyme and microbial activities, gases, water etc.) across and along roots, 3) temporal changes of the parameters and processes with root growth as well as with water and C flows. In situ techniques: planar optodes, zymography, sensitive gels, 14C and neutron imaging as well as destructive approaches (thin layer slicing) have been used to analyze the rhizosphere extent and the gradients of various physico-chemical and biological characteristics: pH, CO2, O2, redox potential, enzyme activities, content of water, nutrients and excess elements, and organic compounds. A literature analysis allows the conclusion that: i) the rhizosphere extent for most of the parameters assessed by non-destructive visualization techniques is 0.5–4 mm but exceeds 4 mm for gases, nitrate, water and redox potential. ii) The rhizosphere extent of nutrients (N, P) is decoupled from the extent of the corresponding enzyme activities. iii) The imbalance between element flows to and uptake by roots may lead to accumulation of excess elements and formation of root carapaces (e.g. CaCO3 rhizoliths, Fe plaque) ranging up to a few cm. iv) All destructive approaches show a much (3–5 times) larger rhizosphere extent compared to visualization techniques. These conclusions are crucial for a mechanistic understanding of rhizosphere properties and functioning, estimation of the nutrient stocks available to roots, and for rhizosphere modelling considering root growth and architecture. Overall, roots function as ecosystem engineers and build their environment, serving as the main factors shaping rhizosphere extent. Sharp gradients are formed within a few days for nutrients and enzymes, but more time is necessary for the establishment of specific microbial communities. Despite the very strong dynamics of most parameters, their stationarity is reached within a few days because the release of C and enzymes or nutrient uptake are very quickly compensated by utilization by surrounding microorganisms or/and sorption and diffusion processes. We conclude that despite the dynamic nature of each property, the rhizosphere gradients, their extent and shape are quasi-stationary because of the opposite directions of their formation processes.

Rhizosphere size and shape: Temporal dynamics and spatial stationarity

Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria and Bacteroidetes), and Gemmatimonas, Flavobacterium and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization management and provides certain theoretical support for selection of rational fertilization strategies.

/pdf/bacterial-community-structure-after-long-term-organic-and-1t7a8hjf97.pdf

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations.

Summary
Healthy soils that contain an active microbiome and food web are critical to sustainably produce food for a growing global human population. Many studies have focussed on the role of microbial species diversity and the presence of key functional groups as important controls on the many functions that a sustainable food system relies on.
Here, we synthesise recent ecological empirical evidence and theory to propose that the interactions between organisms in the soil food web are the critical determinant of soil function.
We propose the Rhizosphere Interactions for Sustainable Agriculture Model, in which crop roots recruit small, modular, highly connected soil rhizosphere networks from large, static, relatively unconnected and diverse bulk soil networks. We argue that conventional agricultural management disrupts the connections between rhizosphere and bulk soil networks.
Synthesis. We identify future research directions for optimising ecological connections between roots and rhizosphere microbial and faunal networks, and between rhizosphere networks and bulk soil networks in agricultural production systems. Knowledge on these connections can be applied in agricultural systems to sustainability produce food for a growing global population.

/pdf/below-ground-connections-underlying-above-ground-food-17uc1vosm8.pdf

Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere

The microbiomes inhabiting plant roots and their adjacent soil environment play significant roles in plant growth, health, and ecological services. Recent studies have provided detailed insights into many phytomicrobiomes, but our understanding of the root-associated microbiomes of perennial ryegrass is still very limited. Here we carried out a stratified rhizobox experiment involving a fluvo-aquic soil and red soil under elevated (750 ppm) and ambient (350–400 ppm) CO2, and used deep amplicon sequencing to investigate the ryegrass root-associated bacterial microbiomes across compartments (the bulk soil, 2-mm outer rhizosphere, rhizosphere, rhizoplane, and endosphere). We observed increased relative abundances of Proteobacteria (mainly Rhizobiaceae and Enterobacteriaceae) in the rhizosphere, rhizoplane, and endosphere compared with the bulk soil and outer rhizosphere. The dominant bacterial genera (mainly Methylobacterium, Rhizobium, Pseudomonas, Stenotrophomonas, and Enterobacter) which facilitate plant growth and soil nutrient cycling were enriched in the rhizosphere, rhizoplane, and endosphere compared with outer rhizosphere. PICRUSt predicted moderate functional differentiation of bacterial microbiomes across compartments. The bacterial α-diversity showed a decreased trend along a spatial gradient from the bulk soil to the endosphere. The β-diversity and network analyses indicated significant differences in the root-associated bacterial microbiomes between the fluvo-aquic soil and red soil. In conclusion, our study suggests that the filtration and acquisition of the ryegrass root-associated bacterial microbiomes are largely controlled by indigenous soil microbial communities, rather than the changes in root rhizodeposition caused by elevated CO2.

Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass

The regulatory gate hypothesis considers that soil organic C mineralization is a two-step process, where stable C is firstly transformed abiotically and is only then a microbially available substrate. The mechanisms involved in the abiotic conversion of non-microbially available to available soil organic C remain largely unknown. We conducted a perfusion experiment using a repeated fumigated-incubated soil and the corresponding fresh soil. We found that repeated fumigation-incubation significantly decreased soil microbial ATP to 0.22 nmol g−1 soil, 10% of that in the fresh soil, and significantly destroyed microbial composition and diversity. However, it had little influence on the soil CO2-C evolution rate after the flush of fumigant-killed dead biomass (8 μg CO2-C g−1 soil day−1) or dissolved organic C (DOC) concentration (about 7 μg C g−1 soil) and composition during long-term perfusion. We conclude that soil CO2 evolution rate and DOC generation were not regulated by the size or composition of the soil microbial communities. This is in support of the regulatory gate hypothesis. We suggest that abiotic processes in soil organic C mineralization need to be considered more and studied further.

Soil biochemical properties and bacteria community in a repeatedly fumigated-incubated soil

Abiotic processes dominate soil organic matter mineralization: Investigating the regulatory gate hypothesis by inoculating a previously fumigated soil with increasing fresh soil inocula

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Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass

Soil biochemical properties and bacteria community in a repeatedly fumigated-incubated soil

Abiotic processes dominate soil organic matter mineralization: Investigating the regulatory gate hypothesis by inoculating a previously fumigated soil with increasing fresh soil inocula