On Maintenance and Metabolisms in Soil Microbial Communities

Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.

Pelatihan dan ToT Ekologi Tanah untuk Penguatan Pertanian Organik pada Kelompok Tani Al-Barokah dan Walisongo di Desa Ketapang

<p><em><strong>Soil Ecology Training and ToT for Strengthening Organic Agriculture in Al-Barokah and Walisongo Farmer Groups in Ketapang Village</strong>. </em>In sustainable integrated agriculture, farmers are expected to be experts in managing agricultural ecosystems. To support this, training and empowerment of sustainable agricultural management can be carried out for farmers. The process of soil ecology training and training of trainers (ToT) is directed at strengthening organic farming and it is hoped that farmers can play a role as a farm manager, able to stand parallel and have an active relationship with the community and have a role in the system built by the community. Therefore, it is proposed the title of PKM-Training and ToT of Ecology Soil for Strengthening Organic Agriculture. The purpose of training and soil ecology ToT for strengthening organic agriculture is to increase farmers' understanding of the importance of ecology in soil management that has been applied so that there is renewal in soil management and building farmer knowledge. Through the Participatory Action Program approach, the Al-Barokah and Walisongo Farmer Groups farmers are very enthusiastic, which is indicated by an increase in understanding of soil ecology. Training and soil ecology ToT for farmers is very important so that soil management is in harmony with nature and increase the understood that soil ecology is part of the global ecosystem, and soil ecology is a process of interaction between ecological components on the level of fertility and crop production.</p>

Identification of the Park Grass Experiment soil metaproteome

The Park Grass Experiment, is an international reference soil with an impressive repository of temperate grassland metadata, however, it still lacks documentation of its soil metaproteome. The identification of these proteins is crucial to our understanding of soil ecology and their role in major biogeochemical processes. However, protein extraction can be fraught with technical difficulties including co-extraction of humic material and lack of a compatible databases to identify proteins. To address these issues, we used two compatible soil protein extraction techniques on Park Grass soil, one that removed humic material, namely a modified freeze-dry, heat,thaw, phenol, chloroform (HTPC) method and another which co-extracted humic material, namely an established surfactant method. Proteins were identified by matching mass spectra against a tailored Park Grass metagenome database. We identified a broad range of proteins from Park Grass soil, mainly in protein metabolism , membrane transport, carbohydrate metabolism, respiration and ribosome associated categories, enabling reconstitution of specific processes active in grassland soil. The soil microbiome was dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phyla level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to identify many proteins in regulatory and signalling networks of key biogeochemical cycles such as the nitrogen cycle. The combined extraction methods connected previous Park Grass metadata with the metaproteome, biogeochemistry and soil ecology. This could provide a base on which future targeted studies of important soil processes and their regulation can be built.

A Challenge and Chance for Soil Ecology

The understanding of soil and its response to the global warming is important for the harmony of human and environment. Generally, soil has four majorcomponents as air, water, mineral matter, and organic matter. The relative proportions of these four components greatly influence the behavior and productivity of soils. Through interactions of energy flow and mass exchange,soil plays the role as the crucial interface medium for air, minerals, water and life, and forms a complex integrated body, ecosystem. To a great extent, soil ecology is one new branch of ecology that study the relationship between soil biota and environment, including ecological structure, function, balance and evolution of soil ecosystem. The application of soil ecology will be a benefit for the reasonable and sustainable use of land resources and be important for agriculture, forestry and grazing production.

A monodominância da aroeira (Myracrodruon urundeuva (Engler) Fr. Allemão) como determinante da ecologia do solo / The aroeira’s (Myracrodruon urundeuva (Engler) Fr. Allemão) monodominace as soil ecology determinant

Invasões biológicas e as monodominâncias de espécies vegetais podem alterar as propriedades físico-químicas e biológicas do solo, afetando a sua microbiota, que é um importante indicador da sanidade desse ambiente. A aroeira (Myracrodruon urundeuva) é uma espécie arbórea que ocorre em monodominâncias na região do Médio Rio Doce (Minas Gerais), e sua elevada densidade vem acarretando sérios problemas socioambientais. Grandes áreas do município de Tumiritinga-MG estão tomadas por aroeirais e são visualmente perceptíveis diferenças entre o solo das áreas monodominadas por aroeiras e solos sob vegetação nativa. Para investigar se as altas densidades dessas árvores estão causando alterações nas propriedades biológicas do solo sob elas, as comunidades de bactérias, fungos e actinomicetos foram avaliados e raízes de aroeiras foram investigadas a procura de infecções por Fungos Micorrízicos Arbusculares (FMA). Foi constatado que solos sob monodominância das aroeiras são microbiologicamente mais pobres, havendo menor densidade de bactérias, fungos e actinomicetos do que nos solos sob a mata. Também foram encontrados esporos de FMA nos solos dos aroeirais, mas não foram encontradas raízes de aroeira colonizadas por esses fungos. Para avaliar a infectividade desses esporos, substratos estéreis foram inoculados com esporos provenientes dos aroeirais, onde foram colocadas plantas teste para crescer. Decorrido o tempo experimental, não houve colonizações das raízes dessas plantas por FMA. Os resultados obtidos permitiram concluir que a alta abundância da aroeira está afetando negativamente a microbiota do solo, o que pode estar favorecendo o estabelecimento das aroeiras em detrimento de outras espécies, por um efeito de feed-back positivo.

Pivot burrowing of scarab beetle (Trypoxylus dichotomus) larva

Many organisms live in the soil but only a little is known about their ecology especially movement style. Scarab beetle larvae do not have appendages to shovel soil and their trunk is thick compared to their body length. Hence, their movement through the soil is perplexing. Here, we established the observation and analysis system of larval movement and found that the last larval instars of Trypoxylus dichotomus burrow in two different ways, depending on the hardness of the soil. If the soil is soft, the larvae keep their body in a straight line and use longitudinal expansion and contraction; if the soil is hard, they flex and rotate their body. It is thought that the larvae adapt to diverse soil conditions using two different excavation methods. These results are important for understanding the soil ecology and pose a challenge to engineer of newer excavation technology.