The principles of classification and a classification of mammals. Bulletin of the AMNH ; v. 85

The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities.

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Virioplankton: viruses in aquatic ecosystems

The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.

Ecology of prokaryotic viruses

Nitrogen Metabolism in the Rumen

Agriculture, Forestry, and Other Land Use (AFOLU) is unique among the sectors considered in this volume, since the mitigation potential is derived from both an enhancement of removals of greenhouse gases (GHG), as well as reduction of emissions through management of land and livestock (robust evidence; high agreement). The land provides food that feeds the Earth’s human population of ca. 7 billion, fibre for a variety of purposes, livelihoods for billions of people worldwide, and is a critical resource for sustainable development in many regions. Agriculture is frequently central to the livelihoods of many social groups, especially in developing countries where it often accounts for a significant share of production. In addition to food and fibre, the land provides a multitude of ecosystem services; climate change mitigation is just one of many that are vital to human well-being (robust evidence; high agreement). Mitigation options in the AFOLU sector, therefore, need to be assessed, as far as possible, for their potential impact on all other services provided by land. [Section 11.1]

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Agriculture, Forestry and Other Land Use (AFOLU)

Nutrient requirements of domesticated ruminants.

Feeding Standards for Australian Livestock Ruminants.

1. To obtain a quantitative model for nitrogen pathways in sheep, a study of ammonia and urea metabolism was made by using isotope dilution techniques with [15N]ammonium sulphate and [15N]urea and [14C]urea.2. Single injection and continuous infusion techniques of isotope dilution were used for measuring ammonia and urea entry rates.3. Sheep were given 33 g of chaffed lucerne hay every hour; the mean dietary N intake was 23.4 g/d.4. It was estimated that 59% of the dietary N was digested in the reticulo-rumen; 29% of the digested N was utilized as amino acids by the micro-organisms, and 71% was degraded to ammonia.5. Of the 14.2 g N/d entering the ruminal ammonia pool, 9.9 g N/d left and did not return to the pool, the difference of 4.3 g N/d represented recycling, largely within the rumen itself (through the pathways: ruminal ammonia → microbial protein → amino acids → ammonia).6. Urea was synthesized in the body at a rate of 18.4 g N/d from 2.0 g N/d of ammonia absorbed through the rumen wall and 16.4 g N/d apparently arising from deamination of amino acids and ammonia absorbed from the lower digestive tract.7. In the 24 h after intraruminal injection of [15N]ammonium salt, 40–50% of the N entering the plasma urea pool arose from ruminal ammonia; 26% of the 15N injected was excreted in urinary N.8. Although 5.1g N/d as urea was degraded apparently in the digestive tract, only 1.2g N/d appeared in ruminal ammonia; it is suggested that the remainder may have been degraded in the lower digestive tract.9. A large proportion of the urea N entering the digestive tract is apparently degraded and absorbed and the ammonia incorporated in the pools of nitrogenous compounds that turn over only slowly. This may be a mechanism for the continuous supply to the liver of ammonia for these syntheses.10. There was incorporation of 15N into bacterial fractions isolated from rumen contents after intraruminal and intravenous administration of [15N]ammonium salts and [15N]urea respectively.11. A model for N pathways in sheep is proposed and, for this diet, many of the pool sizes and turn-over rates have been either deduced or estimated directly.

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Dynamic aspects of ammonia and urea metabolism in sheep

In Australia, agriculture is responsible for ~17% of total greenhouse gas emissions with ruminants being the largest single source. However, agriculture is likely to be shielded from the full impact of any future price on carbon. In this review, strategies for reducing ruminant methane output are considered in relation to rumen ecology and biochemistry, animal breeding and management options at an animal, farm, or national level. Nutritional management strategies have the greatest short-term impact. Methanogenic microorganisms remove H2 produced during fermentation of organic matter in the rumen and hind gut. Cost-effective ways to change the microbial ecology to reduce H2 production, to re-partition H2 into products other than methane, or to promote methanotrophic microbes with the ability to oxidise methane still need to be found. Methods of inhibiting methanogens include: use of antibiotics; promoting viruses/bacteriophages; use of feed additives such as fats and oils, or nitrate salts, or dicarboxylic acids; defaunation; and vaccination against methanogens. Methods of enhancing alternative H2 using microbial species include: inoculating with acetogenic species; feeding highly digestible feed components favouring ‘propionate fermentations’; and modifying rumen conditions. Conditions that sustain acetogen populations in kangaroos and termites, for example, are poorly understood but might be extended to ruminants. Mitigation strategies are not in common use in extensive grazing systems but dietary management or use of growth promotants can reduce methane output per unit of product. New, natural compounds that reduce rumen methane output may yet be found. Smaller but more permanent benefits are possible using genetic approaches. The indirect selection criterion, residual feed intake, when measured on ad libitum grain diets, has limited relevance for grazing cattle. There are few published estimates of genetic parameters for feed intake and methane production. Methane-related single nucleotide polymorphisms have yet to be used commercially. As a breeding objective, the use of methane/kg product rather than methane/head is recommended. Indirect selection via feed intake may be more cost-effective than via direct measurement of methane emissions. Life cycle analyses indicate that intensification is likely to reduce total greenhouse gas output but emissions and sequestration from vegetation and soil need to be addressed. Bio-economic modelling suggests most mitigation options are currently not cost-effective.

John Nolan

Papers

Nutrient requirements of domesticated ruminants.

Feeding Standards for Australian Livestock Ruminants.

Nitrogen Metabolism in the Rumen

Dynamic aspects of ammonia and urea metabolism in sheep

Ruminant enteric methane mitigation: a review