developed [40]. Nowadays, AMF assemblages are no longer studied only in plant roots, but also in the bulk soil [41–43]. The main result obtained from the application of NGS to the study of AMF biodiversity has been the discovery of an unpredictable diversity within the Glomer‐ omycota phylum [39]. However, this series of innovative molecular tools has introduced a new issue, that is, the continuously increasing number of unidentified AMF DNA sequences from environmental samples with no correspondence whatsoever to sequences of known species [44]. This has naturally made scientists aware of the fact that the number of AMF species could be larger than expected. However, it is not reliable to have new species described on just the basis of short DNA sequences obtained by means of NGS tools. Instead, for each new suggested taxon, a series of steps needs to be followed to characterize the morphotype, the functional traits, and the ecological role offered when present in combination with other organisms in a given environment. Therefore, NGS tools cannot be considered as complete replacements of the traditional methods of identification and description of new species. The combined approach is still necessary to shed light on such a key group of organisms and to make them available for agricultural application and, more in general, for other practices useful for the wellbeing of humankind [45].

**1. Reference 2. Year 3. Method 4. Target**

**region**

[53] <sup>2012</sup> Clon-seq SSU Plant root Alpine meadow

[51] 2012 NGS SSU Soil

[54] 2011 NGS SSU Plant root

[55] 2011 NGS SSU Plant root

[56] 2011 Clon-seq SSU Plant root

[41] 2010 NGS SSU Soil

[59] 2009 Clon-seq SSU Plant root

[60] 2009 NGS SSU Plant root

[62] 2008 Clon-seq SSU Plant root

[65] 2008 Clon-seq SSU Plant root

[67] 2007 Clon-seq SSU Rhizoids

[66] 2007 Clon-seq ITS

**5. Studied compartment**

[52] 2012 NGS LSU Plant root Grassland (Denmark) 82511 32 [42] 2012 Clon-seq SSU/LSU Soil and plant root Arable field (Italy) 427/364 20/23a

[57] 2010 Clon-seq SSU Soil and plant root Vineyard (Italy) 681 37 [58] 2009 Clon-seq SSU Plant root Woodland (UK) 617 33/37b

[61] 2008 Clon-seq LSU Soil and plant root Arable field (Italy) 183 8

[63] 2008 Clon-seq SSU Plant root Arable field (Mexico) 213 16

Soil, plant root and spores

[64] <sup>2008</sup> Clon-seq SSU Plant root Serpentine soils

**6.Ecosystem**

Arbuscular Mycorrhizal Fungi and their Value for Ecosystem Management

Prairie - Chernozem (Cananda)

ecosystem (China)

Broadleaf, mixed broadleaf and coniferous forests, botanical gardens, greenhouse

Grassland, wood and heath (UK)

Hardwood forest (USA)

Mediterranean soils (Italy)

Mediterranean semiarid soils (Spain)

> Boreal forest (Estonia)

> Boreal forest (Estonia)

> > (USA)

Arable field (Sweden)

Liverworts (Worldwide)

**7. AMF sequences**

http://dx.doi.org/10.5772/58231

7086 33

4452 38

65001 73

108245 70

1598 17

2815 19/80a

1443 21

111580 47

911 26/27c

1249 19

115 8

150 10

Meadow (Germany) 180 >18

**8. OTUs**

165



developed [40]. Nowadays, AMF assemblages are no longer studied only in plant roots, but also in the bulk soil [41–43]. The main result obtained from the application of NGS to the study of AMF biodiversity has been the discovery of an unpredictable diversity within the Glomer‐ omycota phylum [39]. However, this series of innovative molecular tools has introduced a new issue, that is, the continuously increasing number of unidentified AMF DNA sequences from environmental samples with no correspondence whatsoever to sequences of known species [44]. This has naturally made scientists aware of the fact that the number of AMF species could be larger than expected. However, it is not reliable to have new species described on just the basis of short DNA sequences obtained by means of NGS tools. Instead, for each new suggested taxon, a series of steps needs to be followed to characterize the morphotype, the functional traits, and the ecological role offered when present in combination with other organisms in a given environment. Therefore, NGS tools cannot be considered as complete replacements of the traditional methods of identification and description of new species. The combined approach is still necessary to shed light on such a key group of organisms and to make them available for agricultural application and, more in general, for other practices useful for the

> **5. Studied compartment**

[46] 2013 NGS SSU Soil Prairie (Cananda) 1335521 120

[49] 2013 Clon-seq SSU Soil and plant root Prairie (USA) 232 13 [43] 2012 NGS SSU Soil Forest (Estonia) 13320 37 [50] 2012 NGS SSU Soil Arable field (China) 59611 70

SSU Plant root

[47] <sup>2013</sup> NGS SSU Plant root and Soil Temperate forest

[48] 2013 Clon-seq SSU Plant root

**6.Ecosystem**

Tropical, subtropical, temperate and boreal forests, subtropical and temperate grasslands, tropical and subtropical deserts and shrublands, and polar tundras (Africa, Asia, Oceania, Europe, North and South America)

(Estonia)

Mediterranean semiarid soils (Spain)

**7. AMF sequences**

2353/22391 204

35738 76

467 30

**8. OTUs**

wellbeing of humankind [45].

164 Biodiversity - The Dynamic Balance of the Planet

[39] 2013

**1. Reference 2. Year 3. Method 4. Target**

Clonseq/NGS **region**


Ecosystem from which the samples were collected, 7. Number of DNA sequences and 8. OTUs (Operational Taxonomic

Arbuscular Mycorrhizal Fungi and their Value for Ecosystem Management

http://dx.doi.org/10.5772/58231

167

Most human activities have an arguable impact on the physical and biological aspects of soil. As mentioned before, AMF are among the most widespread soil microorganisms, and each human activity that has an impact on soil, such as agricultural practices, therefore has a side effect on them. These practices, alone or in combination, exert an enormous selective pressure on AMF that shapes their community structure and evolution by modifying several of their biological features, such as sporulation strategy, resource allocation and spatial distribution [86]. As in natural ecosystems, AMF are also present and active in agricultural ecosystems, where they colonize several major arable crops (sorghum, maize, wheat and rice). Many studies have indicated that AMF diversity, effectiveness, abundance and biodiversity decline in agroecosystems subjected to high input practices [41,42]. Modern intensive farming practices that implement deep and frequent tillage, high input inorganic fertilization and pesticide use are evidently a particular threat to AMF. This is surely a drawback for agriculture, since the more AMF biodiversity losses, the fewer AMF functional traits the host plant can benefit from. On the other hand, the activity and diversity of AMF, following conversion from conventional to organic farming, have not yet been investigated thoroughly. However, the available data seem to indicate that AMF respond positively to the transition to organic farming through a progressive enhancement of their activity [87]. Even though it is difficult to dis‐ criminate between the effects that different agricultural treatments exert on AMF communities, they are here considered separately, and their role in shaping AMF communities will be

One of the most ancient and representative agricultural techniques is tillage. Tillage has played a crucial role in the evolution and technological development of agriculture, particularly for food production. The benefits produced by tillage include a better conservation of water and soil fertility, the abatement of weeds and the preparation of a suitable seedbed. To fulfill these tasks, the undisturbed soil is mechanically manipulated in an effort to modify the physical characteristic of the soil and eliminate weeds. The physical, chemical and biological effects of tillage on the soil can be both beneficial and negative, depending on the methods that are used. The inappropriate use of tillage techniques can therefore have a dramatic impact on the soil structure and on soil microorganism community assemblage. It is possible to identify different tilling levels, ranging from a very low impact, "No-tillage", to a high impact, "conventional tillage". A continuum of intermediate conditions lies in between these two extreme situations,

The mechanical soil disturbance experienced by AMF in tilled agricultural soils has no equivalent in natural ecosystems. This is why tillage has been widely recognized to be one of the principal causes of the modification of the AMF communities that colonize plant roots in

Units) from arbuscular mycorrhizal fungi.

analyzed.

**2. The impact of humans on AMF biodiversity**

**2.1. Tillage: A conventional practice detrimental to AMF**

e.g. varying frequency and intensity of the plowing.

a-taxa obtained with different primer sets; b: taxa obtained at different study sites; c-taxa obtained from forest ecosystems of different ages and management intensities; d-taxa obtained from roots of different plant species; e-taxa obtained at different sampling times.

**Table 1.** The table shows an overview of DNA-based studies on the diversity of Arbuscular Micorrhizal (AM) fungal communities. For each study, the following are reported in sequence: 1. Reference, 2. Year of publication, 3. Used method (Clon-seq=cloning and sequencing; NGS=next generation sequencing), 4. Studied DNA region (SSU=Small Subunit; LSU=Large Subunit, ITS=Internal Transcribed Spacer), 5. Compartment from which the DNA was analyzed, 6. Ecosystem from which the samples were collected, 7. Number of DNA sequences and 8. OTUs (Operational Taxonomic Units) from arbuscular mycorrhizal fungi.
