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

Nutrient cycles link agricultural systems to their societies and surroundings; inputs of nitrogen and phosphorus in particular are essential for high crop yields, but downstream and downwind losses of these same nutrients diminish environmental quality and human well-being. Agricultural nutrient balances differ substantially with economic development, from inputs that are inadequate to maintain soil fertility in parts of many developing countries, particularly those of sub-Saharan Africa, to excessive and environmentally damaging surpluses in many developed and rapidly growing economies. National and/or regional policies contribute to patterns of nutrient use and their environmental consequences in all of these situations ( 1 ). Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.

/pdf/nutrient-imbalances-in-agricultural-development-5c0etk763p.pdf

Nutrient Imbalances in agricultural development

This introductory text on the design and analysis of sample surveys emphasizes the practical aspects of survey problems. It begins with brief chapters on the role of sample surveys in the modern world. Thereafter, each chapter introduces a sample survey design or estimation procedure by describing the pertinent practical problem. The authors describe the methodology proposed for solving the problem and provide the details of the estimation procedure, including a compact presentation of the formulas needed to complete the analysis. Then, a practical example is worked out in complete detail. At the end of each chapter, a wealth of exercises gives students ample opportunity to practice the techniques and stretch their grasp of ideas.

Elementary Survey Sampling

Gaseous ammonia (NH3) is the most abundant alkaline gas in the atmosphere. In addition, it is a major component of total reactive nitrogen. The largest source of NH3 emissions is agriculture, including animal husbandry and NH3-based fertilizer applications. Other sources of NH3 include industrial processes, vehicular emissions and volatilization from soils and oceans. Recent studies have indicated that NH3 emissions have been increasing over the last few decades on a global scale. This is a concern because NH3 plays a significant role in the formation of atmospheric particulate matter, visibility degradation and atmospheric deposition of nitrogen to sensitive ecosystems. Thus, the increase in NH3 emissions negatively influences environmental and public health as well as climate change. For these reasons, it is important to have a clear understanding of the sources, deposition and atmospheric behaviour of NH3. Over the last two decades, a number of research papers have addressed pertinent issues related to NH3 emissions into the atmosphere at global, regional and local scales. This review article integrates the knowledge available on atmospheric NH3 from the literature in a systematic manner, describes the environmental implications of unabated NH3 emissions and provides a scientific basis for developing effective control strategies for NH3.

Ammonia in the atmosphere: a review on emission sources, atmospheric chemistry and deposition on terrestrial bodies.

Effects of varying dietary protein and energy levels on the production of lactating dairy cows.

Prediction of manure and nutrient excretion from dairy cattle.

Effects of Dietary Nitrogen Manipulation on Ammonia Volatilization from Manure from Holstein Heifers

/pdf/animal-diet-modification-to-decrease-the-potential-for-1kpfc2ceen.pdf

Animal Diet Modification to Decrease the Potential for Nitrogen and Phosphorus Pollution

Improved sequencing and analytical techniques allow for better resolution of microbial communities; however, the agriculture field lacks an updated analysis surveying the fecal microbial populations of dairy cattle in California. This study is a large-scale survey to determine the composition of the bacterial community present in the feces of lactating dairy cattle on commercial dairy operations. For the study, ten dairy farms across northern and central California representing a variety of feeding and management systems were enrolled. The farms represented three typical housing types including five freestall, two drylot and three pasture-based management systems. Fresh feces were collected from 15 randomly selected cows on each farm and analyzed using 16S rRNA gene amplicon sequencing. This study found that housing type, individual farm, and dietary components significantly affected the alpha diversity of the fecal microbiota. While only one Operational Taxonomic Unit (OTU) was common among all the sampled individuals, 15 bacterial families and 27 genera were shared among 95% of samples. The ratio of the families Coriobacteriaceae to Bifidobacteriaceae was significantly different between housing types and farms with pasture fed animals having a higher relative abundance of Coriobacteriaceae. A majority of samples were positive for at least one OTU assigned to Enterobacteriaceae and 31% of samples contained OTUs assigned to Campylobacter. However, the relative abundance of both taxa was < 0.1%. The microbial composition displays individual farm specific signatures, but housing type plays a role. These data provide insights into the composition of the core fecal microbiota of commercial dairy cows in California and will further generate hypotheses for strategies to manipulate the microbiome of cattle.

/pdf/fecal-microbial-communities-in-a-large-representative-cohort-2107a8z0ci.pdf

Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows

Particle size was quantified in dairy manure from three different age groups; lactating cows, heifers, and calves. Manure was separated according to five different screen sizes: 2.0, 1.0, 0.5, 0.25, and 0.125 mm. The material on each screen was analyzed for Total Solids (TS), Nitrogen (N), Phosphorus (P), and Potassium (K). The majority of nutrients in the manure were found to be associated with particle sizes smaller than 0.125 mm, specifically 86% of N, 85% of P, and 99.8% of K. Furthermore, particle sizes smaller than 0.125 mm accounted for 46% of TS. Maximum expected removals with standard mechanical separators used on dairy farms would be 19% TS and 5% of N, 5% of P, and 0.07% of K excreted as fresh manure when 2.0-mm screen is used. Maximum anticipated removal when a double screen separator system is used is 31% of TS, 7% of N, 7% of P, and 0.09% of K excreted as fresh manure with both the 2.0- and 1.0- mm screens. Actual removal values under field conditions would vary depending on particle size and quantity of bedding used.

Deanne Meyer

Papers

Prediction of manure and nutrient excretion from dairy cattle.

Effects of Dietary Nitrogen Manipulation on Ammonia Volatilization from Manure from Holstein Heifers

Animal Diet Modification to Decrease the Potential for Nitrogen and Phosphorus Pollution

Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows

Particle Size and Nutrient Distribution in Fresh Dairy Manure