The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

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ARB: a software environment for sequence data

Instead of containing stable and chemically unique ‘humic substances’, as has been widely accepted, soil organic matter is a mixture of progressively decomposing organic compounds; this has broad implications for soil science and its applications. The exchange of nutrients, energy and carbon between soil organic matter, the soil environment, aquatic systems and the atmosphere is important for agricultural productivity, water quality and climate. Long-standing theory suggests that soil organic matter is composed of inherently stable and chemically unique compounds. Here we argue that the available evidence does not support the formation of large-molecular-size and persistent ‘humic substances’ in soils. Instead, soil organic matter is a continuum of progressively decomposing organic compounds. We discuss implications of this view of the nature of soil organic matter for aquatic health, soil carbon–climate interactions and land management. Soil organic matter contains a large portion of the world's carbon and plays an important role in maintaining productive soils and water quality. Nevertheless, a consensus on the nature of soil organic matter is lacking. Johannes Lehmann and Markus Kleber argue that soil organic matter should no longer be seen as large and persistent, chemically unique substances, but as a continuum of progressively decomposing organic compounds.

The contentious nature of soil organic matter

SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and oftenconfusingterminologyaswellasunnecessarilypolarizingdebates. Thus,wereviewrecentliteratureonmicrobialcommunityassembly, using the framework of Vellend (Q. Rev. Biol. 85:183‐206, 2010) in an effort to synthesize and unify these contributions. We begin by discussingpatternsinmicrobialbiogeographyandthendescribefour basic processes (diversification, dispersal, selection, and drift) that contributetocommunityassembly.Wealsodiscussdifferentcombinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generatehypothesesdescribinghowthesedifferencesmaybeimportantforcommunityassembly.Weendbydiscussingtheimplications ofmicrobialassemblyprocessesforecosystemfunctionandbiodiversity.

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Patterns and Processes of Microbial Community Assembly

Occurrences and removal of pharmaceuticals and personal care products (PPCPs) in drinking water and water/sewage treatment plants: A review

Development of Biochar-Based Functional Materials: Toward a Sustainable Platform Carbon Material

Many iron (Fe) redox processes that were previously assumed to be purely abiotic, such as photochemical Fe reactions, are now known to also be microbially mediated. Owing to this overlap, discerning whether biotic or abiotic processes control Fe redox chemistry is a major challenge for geomicrobiologists and biogeochemists alike. Therefore, to understand the network of reactions within the biogeochemical Fe cycle, it is necessary to determine which abiotic or microbially mediated reactions are dominant under various environmental conditions. In this Review, we discuss the major microbially mediated and abiotic reactions in the biogeochemical Fe cycle and provide an integrated overview of biotic and chemically mediated redox transformations.

The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle

Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil.

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Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

Biochar influences soil fertility, N2O emissions, and atmospheric CO2 budgets, and because of its quinone and aromatic structures, it is redox-active. Here we demonstrate that biochar concentrations of 5 and 10 g L–1 stimulate both the rate and the extent of microbial reduction of the Fe(III) oxyhydroxide mineral ferrihydrite (15 mM) by Shewanella oneidensis MR-1, while lower biochar concentrations (0.5 and 1 g L–1) have a negative effect on ferrihydrite reduction. Control experiments showed that biochar particles and not biochar-derived water-soluble organic compounds are responsible for the stimulating and inhibiting effect. We also found that biochar changed the mineral product of ferrihydrite reduction from magnetite (Fe3O4) to siderite (FeCO3). Our study suggests that biochar can influence soil biogeochemistry not only indirectly by changing the soil structure and chemistry but also by directly mediating electron transfer processes, i.e., by functioning as an electron shuttle.

Sebastian Behrens

Papers

The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

Biochar as an Electron Shuttle between Bacteria and Fe(III) Minerals

The identification of microorganisms by fluorescence in situ hybridisation.