Soil microbiology and molecular biology

Organisms that live in the soil, in particular microorganisms forming complex populations, and with advances in molecular biology have discovered even more complex levels of diversity. Since, most of the prokaryote organisms are not able to grow on artificial media (^{Nogales, 2005}), from the discovery of molecular markers such as phospholipid fatty acids (PLFA) and nucleic acids (DNA and RNA) (^{Insam, 2001}, ^{Kirk et al., 2004}) have made ​significant progress in the study of these organisms. The combined use of different molecular techniques based on small subunit rRNA has generated important data on diversity, structure and dynamics of microbial communities.

For example, DNA molecular studies have shown that, the clone libraries constructed from soils can be comprised almost entirely of only members of the microbial communities (^{Zhuo et al., 2002}). Indeed, ^{Fierer et al. (2007)} used sequence analysis based on small subunit rRNA and meta-genomics and reported that, the communities of archaea and fungi are more regular and constant. Towards the interior of the four comparison groups (fungi, bacteria, archaea and viruses) few overlaps were observed in the taxonomy of the sampling sites, suggesting that these groups are very diverse both locally and globally. The great diversity is found because some qualitative properties of the soil matrix promote the development and maintenance of these communities. The vast majority of communities are scarce, and few are the most abundant, suggesting competitive interactions that determine their structures (^{Zhuo et al., 1997}), especially in saturated soil, compared to surface soils where there is no dominant competition between communities.

Two of the features that promote this diversity are the stability of soil moisture in deeper layers, and high competition for carbon sources not as abundant as in surface layers. It has also been shown that the diversity of microorganisms increases with decreasing particle size of the soil (^{Sessitsch et al., 2001}; ^{Tiedje et al., 2001}). In topsoil exists nearly uniform pattern distribution rRNA restriction, indicating that these sites have a high level of microbial diversity, with no dominant group. On the other hand, saturated soils have a lower diversity and higher levels of competition between the communities observed.

The advances that have occurred in design micro-arrays have enabled the analysis of large volumes of data to detect gene expression under certain experimental conditions or to find the presence of sequences under a given experimental sample (^{Murray et al., 2001}; ^{Chang et al., 2008}).

With the sequencing of microbial genomes has been possible to integrate multiple databases (^{Uchiyama et al., 2010}). One of these databases is the Integrated Microbial Genomes, which reports 10 165 microbial genomes sequenced, of which 5131 correspond to bacteria, archaea 196, 188 eukaryotes, plasmids 1 186 and 2 810 viruses (Table 1), and the use of bioinformatics tools and functional genomics is revealing important functional and evolutionary information.

Climbing in the complexity of sequencing projects, meta-genomes (genetic material from an environmental sample) of microbial communities derived from complex processes of direct extraction of DNA from microorganisms that inhabit ecosystems and their rescue and file called meta-genomic libraries contain the full genetic capacity of biological systems as the communities composed of many species, easily accessible for other experiments. In Figure 1, the scheme of the construction and use of meta-displayed libraries.

Figure 1 Construction process and use of meta-libraries of soil samples (modified of ^{Lorenz et al., 2005}). 

Applications of meta- genomics research not only to understand the molecular processes that generate biodiversity but also recreate in the laboratory test conditions for biotechnological purposes such as soil remediation.

The applications under development and looming are immense and the coming changes to these developments placed to scientific research into a new era. With these technologies we can meet structure and function of organisms ever discovered or had not been possible to grow under traditional microbiology techniques. Genome projects led by Craig Venter (^{Venter et al., 2004}) have found more than 782 new genes in photoreceptors, when previously 148 were known (^{Handelsman, 2004}; ^{Seshadri et al., 2007}).

Soil biodiversity and landscape sustainability

Recent scientific advances in genomic science and growth in the number of sequences transcribed genes, proteins and other molecules deposited in public databases is one of the largest carriers that allow the study of soil biodiversity. As the primary sustenance of life on the planet, knowledge of biological diversity in the soil system represents a basis of crucial importance that in turn generates changes in ecosystems over and that may explain the rich landscape that exists on the Earth.

Biodiversity refers to the number and distribution of species in the biosphere. The species of the biosphere are actually the result of processes of evolution and extinction (^{Bridgewater, 1988}, ^{Cardinale et al., 2012}). Criteria for assessing biodiversity are based on quantifying the ecological requirements of the species to establish local ecological, environmental policies, and the empirical data available.

Biodiversity and landscape elements are closely linked. The highest rates of biodiversity arise when landscape patterns and biological processes are more heterogeneous (^{Nichols et al., 1998}). Therefore, landscape development projects must consider the future maintenance of high landscape heterogeneity, which can ensure the highest biodiversity conservation.

According to ^{Mora et al . (2011)}, global biodiversity is comprised of over 1 244 360 classified species, and it is estimated that there are 8.75 million still identify more species on Earth, in addition to about 2.5 million species in the oceans. In order to properly understand and manage biodiversity, it is necessary to place it in the context of the landscape. From the environmental point of view, the landscape is part of the space on the surface of the land that exists as a complex system, formed by the activity of rocks, water, air, plants, animals and man, and that its appearance forms a recognizable entity. Moreover, the landscape is conceived as a grouping of ecosystems, big and small, related to each other in a hierarchy of spaces that can be better understood through indicators such as biota and soil are able to achieve balance to changes energy flows.

In simpler terms, the landscape is a green complex that hosts various biotic and abiotic elements, and in which, for example, animals depend on plants for food and plants can use the animal waste to stock mineral elements nourish them, and which take soil mainly through processes of decomposition and transformation conducting soil organisms. Biodiversity and landscape, therefore, are closely related (^{Waldhardt, 2003}; ^{Johns, 2004}). The landscape pattern is a portion of this particular landscape as the edges of paths or roads in the countryside and mountains, repeated constantly due to the nature of space and involves factors and natural processes that makes a sui generis entity.

The highest rates of biodiversity arise when natural processes and landscape patterns are more heterogeneous. Therefore, development projects of landscape with rich biological communities should consider maintaining a high heterogeneity of its elements so that a wealth of microorganisms that started from the dream to be promoted; this will result in greater assurance of biodiversity conservation (^{Bridgewater, 1988}).

Landscape ecology dimensions incorporates both conservation and use of ecosystems that create sustainable and harmonious environment between man and nature, and one of the ways is through planning (^{Wiens, 2009}).

According to ^{Brown (2013)}, the planning of landscape diversity is a method that allows the planning, design and communicate the benefits and habitats of biological diversity in certain environments. This based on the richness of the landscape system, helpful to carry out projects of conservation, restoration, development and improvement of housing landscape both urban and rural settlements. The leading international sustainable projects are increasingly incorporating elements of native biodiversity for development of landscape. These projects also consider minimizing environmental impact, especially in working with the management of protected species and sensitive natural environments in sustainable strategies and holistic approaches. A sustainable landscape is characterized by including a greater diversity of living organisms, including flora, fauna and interacting elements. This allows heterogeneous communities certainly, but also in a relationship of ecological stability.

A sustainable landscape is dynamic since the interaction of its elements is always undergoing changes (^{Dunnett and Hitchmough, 2004}). It is in here where the importance of replacing the built landscapes conventionally, which are usually low in biodiversity and high costs due to the loss of resources (open system) for sustainable landscapes, which also tend to reuse resources as water, energy, etc. (closed system) (^{Dunnett and Clyden, 2007}). Additionally, through these initiatives can make the projection of landscape development, and demonstrate an improvement in the local ecology.

This is of particular interest in abandoned industrial and urban areas, which are often the focus of conservation groups or sustainable urban development. Therefore, this new approach can serve as a useful tool to quantitatively demonstrate the benefits of smart urban growth and conservative development as a means to exploit local biodiversity and improve management, increase environmental ecosystem services and realize the tool conservative views of the localities.

These efforts address multiple aspects of sustainability such as transport, energy, water, scenery, villages, society, the local economy, among others, and include quantitative measurements of various indicators of sustainability as the emission of greenhouse emissions, energy and water use, fertilizer use, waste management, among many others.

Planning and design systems of landscape biodiversity and landscape biodiversity indices are concepts and approaches that tackle biodiversity issues from the point of view of quantitative measurements. Such quantitative measurements allow developing detailed, comprehensible and defensible estimates of performance of design solutions and planning in terms of both benefits and costs.

The measurement system of the landscape biodiversity index considers the assessment of numerous indicators (up to 10 or more) of landscape biodiversity, these indicators include the structure and characteristic patterns of landscape as a priority species, habitat quality, connectivity and total area of habitat. Genomic sciences can identify and quantify the number and diversity of organisms living in the soil, but also in the water, or the trees themselves and the rhizosphere of the species that exist or are planned to establish in landscape development projects.

With all of this, biodiversity and landscape are interrelated through the landscape patterns and processes. The ideal strategy for maintaining biodiversity is to maintain the landscape with the greatest variation of its elements. It should be emphasized that, the health of the landscape is critical to the maintenance of biodiversity condition and vice versa. The challenges ahead are to ensure that existing landscapes maintain and improve landscape quality through strategies of conservation and restoration of biodiversity. For the success of this company is necessary to work on the maintenance of biodiversity not only at the level of individual species, but through holistic landscape management.

In terms of terrestrial biodiversity, soil is considered the most complex system, and in turn, the life support to enrich the landscape. Genomic sciences that allow the study of the biodiversity of soil environmental samples, provide tools with great potential for better understanding and management of the landscape, providing not only information related organisms that live there, but also what features and play what is its potential use in a sustainable context.

Recently, ^{Gómez-Merino et al . (2013)} conducted an analysis of the strengths and challenges to foster innovation in the landscape in Mexico and conclude that thanks to the mega-diversity with which the country and its genetic and natural resources can contribute to landscape improvement. In terms of basic and applied research, Mexico has made ​significant progress in studies of biodiversity, and has significant infrastructure in various centres and research institutions. In order to generate the transformations required to catapult the use and sustainable management of the landscape, it is necessary to include the issue on the agendas of science, technology and innovation, with a focus on sustainability and social responsibility with scientific basis.