Fusarioid fungi in soils of agroecological polycultures and tropical dry forest in rural Triunfo, Brazil: Insights into sustainable agricultural management

Abstract

This study aimed to identify fusarioid fungi in the soils of sustainably managed agricultural areas and a fragment of the Brazilian Caatinga, both in a semi-arid region of Brazil. We provide a survey of peer-reviewed papers reporting the substrates, hosts, and geographic regions in Brazil in which the identified species were of agricultural interest. Soil samples were collected in July 2019, February 2020, and July 2020 from different agroecosystems and a fragment of the Brazilian Caatinga in rural Triunfo, Brazil. Fusarioid fungi were obtained by serial dilution of soil and colony purification using single-conidial culturing. Maximum likelihood evaluation (ML) based on sequences from the tef1-α gene was used to identify fusarioid fungi. The distribution of these species in other agroecosystems and the natural environment in Brazil was assessed by an extensive search of the literature available in public databases. Fusarium annulatum, F. verticillioides, F. lacertarum, and Neocosmospora vasinfecta were identified. These species are distributed throughout Brazil and are registered as plant pathogens, mainly in areas with conventional agriculture. These data reinforce the importance of sustainable soil management in agricultural areas and expand our knowledge of the behavior of these microorganisms in environments without human interference.

Keywords: Agroforestry; Family farming; Intensive Agriculture; Soil quality indicators; Trophobiosis.

Introduction

Tropical dry forests predominate between approximately 20° N and 30° S in regions with high temperatures, low annual thermal extent, low humidity, and long dry spells. These forests consist of plants adapted to these abiotic conditions. Over time, the replacement of native forest areas by conventional agricultural systems in these regions has caused socioeconomic and environmental problems (Silva and Barbosa, 2017). Sustainable agricultural production proposals, such as agroecological polycultures, have been suggested to mitigate these problems. Agroecological polycultures, such as consortiums of plants (COPs) and agroforestry systems (AFSs), apply sustainable soil and plant management techniques, minimize negative environmental impacts, and favor adaptation to the abiotic conditions of the growing region (Alves et al., 2021).

Fungi generally represent a considerable microbial biomass, varying from 10⁴ to 10⁶ colony-forming units per gram of soil (CFU g^˗1 soil), and they are responsible for producing characteristic physicochemicals in ecosystems, solubilizing nutrients for plants through metabolic activities, participating in energy flow, and structuring soil layers (Alves et al., 2021). Among the commonly isolated soil fungi are fusarioid fungi (Arias Mota and Abarca, 2020; Alves et al., 2021). Although they are cosmopolitan, colonizing different substrates and hosts and providing various niches in ecosystems, special attention has been paid to these fungi because they are phytopathogens that cause significant losses in agricultural production and are important producers of mycotoxins that threaten animal and human food security (O’Donnell et al., 2018; Summerell, 2019).

The term fusarioid fungi refers to organisms distributed in 20 genera in Nectriaceae (Sordariomycetes), including Fusarium. These organisms are morphologically recognized for presenting phialidic asexual morphs with various septate, falcate conidia with diverse degrees of foot-shaped basal cell development, formed on aerial or sporodochia conidiophores. Relying on the species, the production of microconidia can also be observed (Crous et al., 2021). Some species also produce chlamydospores, which can remain dormant in the environment for a long time until favorable conditions cause their reactivation and infection in a host (Yilmaz et al., 2021).

With the growth of phylogenetic studies, Fusarium spp. have been segregated and species that are not phylogenetically related to the sensu stricto group (Gibberella sexual morphs) have been transferred to other fusarioid genera (Crous et al., 2021). The main gene regions used to study fusarioid fungi are the translation elongation factor 1-α (tef1) and the second major subunit of RNA- polymerase II (rpb2); tef1 is the first choice among major studies based on a single locus, such as in gene barcodes, and provides a high-resolution strategy for defining fusarioid genera (Crous et al., 2021).

Although fusarioid fungal colonization is common in agroecosystem soils, few studies have investigated the occurrence of these organisms in areas with sustainable management (Arias Mota and Abarca, 2020; Alves et al., 2021) and native areas (Leslie and Summerell, 2011). Therefore, this study aimed to identify fusarioid fungi within the soil of sustainable agricultural areas, including agroforestry systems and a consortium of plants, as well as in a tropical dry forest fragment of the Brazilian Caatinga. Additionally, it seeks to conduct a comprehensive bibliographic review encompassing substrates, hosts, and geographic regions across Brazil where these species have been reported, correlating the suppression of fungal pathogenicity with plant diversity. This study will expand the knowledge of the biogeography of fusarioid fungi isolated in this research and define the influence of plant hosts and land use on their distribution and ecology, generating information that will aid the sustainable management of agricultural systems (AFS).

Material and methods

Study area

Soil samples were collected from a fragment of the Brazilian Caatinga and agroecological polycultures at the Volta do Enjeitado site, in rural Triunfo, Pernambuco.

The fragment of the Brazilian Caatinga [7°54’52.0”S 38°03’01.2”W (elevation 461 m)], near a farmer’s house. It has been under conservation for 40 years. The only wood that was removed was the plant remains for fence production (Figure 1 A , B). It consisted of small trees and profusely branched shrubs with thorns and small leaves, mixed with succulent plants (generally cacti) and a herbaceous stratum formed by annual plants (mainly therophytes), terrestrial bromeliads, and creeping cacti.

Figure 1.
Areas of different land use at the Volta do Enjeitado site, in rural Triunfo, Pernambuco, Brazil. A-B: Fragment of the Brazilian Caatinga in the dry and precipitation periods, respectively; C-D: Inside and external view of the agroforestry system, 24-year-old, respectively; E-F: Agroforestry system, 8-year-old.

Two types of agroecological polycultures were studied: two AFSs that differed in age and purpose and a COP. An AFS is characterized by the implantation of more than three plant species with the cultivation of trees and herbaceous plants. A COP is characterized by the implantation of two to three plants of short or annual cycle, generally alternating between grasses, legumes, and roots (Alves et al., 2021, 2023). The 24-year-old AFS (AFS24) was approximately 10.000 m² [7°55’05.5”S 38°02’52.2”W (elevation of 453 m)], and was planted by farmers to restore a portion of the riparian forest of the Pajeú River (Figure 1 C , D). The 8-year-old AFS (AFS8) was approximately 2.500 m² [7°55’04.4”S 38°02’55.0”W (elevation of 457 m)], and was planted by farmers with the aim of subsistence (Figure 1 E , F). The COP was approximately 4.500 m² [7°55’03.6”S 38°02’53.4”W (elevation of 457 m)], and had been farmed for 15 years (Figure 2). During this time, farmers primarily raised corn (Zea mays L.) and beans (Phaseolus vulgaris L.), followed by a fallow year, and subsequently, corn with cassava (Manihot esculenta Crantz), watermelon [Citrullus lanatus (Thumb.) Matsum. and Nakai], and palm [Opuntia cochenillifera (L.) Mill.]. Notably, COP and AFSs differed in crop composition. Both had annual or pasture crops. However, AFSs (AFS8 and AFS24) also contained woody plants (Figure 1 C -F). Both AFSs have native plants. However, they predominate in AFS24 to restore the riparian forest. The composition of plants in the studied areas (COP, AFS8, and AFS24) at each collection point is shown in Table 1.

Figure 2.
Area of consortium of plants (COP) (15-year old) at the Volta do Enjeitado site, in rural Triunfo, Pernambuco, Brazil. A: COP (1-year old in fallow) in July 2019. B-C: COP with Zea mays L, palm [Opuntia cochenillifera (L.) Mill.] (Figure 2 B yellow arrow), cassava (Manihot esculenta Crantz) (Figure 2 B yellow asterisk), and watermelon [Citrullus lanatus (Thumb.) Matsum. and Nakai] (Figure 2 C red arrow) in February 2020. D: COP after harvesting in July 2020.

Table 1.
Plant composition of the consortium of plants at 15-year old (COP), of the agroforestry system at 8-year old (AFS8), of the agroforestry system at 24-year old (AFS24) and of the fragment of the Brazilian Caatinga (CA) per sampling plots (represented by geographic coordinates) in the Volta do Enjeitado site, in rural Triunfo, Pernambuco, Brazil.

COP: sampling plot	AFS8: Sampling plot	AFS24: sampling plots	CA: sampling plots
Zea mays L.;	Anacardium occidentale L.	Gliricidia sepium (Jacq.) Kuntd ex Walp	Sideroxylon obtusifolium (Roem. & Schult.) T.D. Penn.
Manihot esculenta Crantz:	Opuntia cochenillifera (L.) Mill.	Opuntia cochenillifera (L.) Mill.	Schinopsis brasiliensis Engl.
	Mimosa caesalpiniifolia Benth.	Triplaris gardneriana Wedd.	Coutarea hexandra Schum.:
	Annona squamosa L.:	Lithrea molleoides (Vell.) Engl.:
7°55′04.0′′S 38°02′54.0′′W	7°55′03.9′′S 38°02′55.1′′W	7°55′06.5′′S 38°02′53.5′′W	7°54′54.2′′S 38°03′00.2′′W
Zea mays L.:	Mangifera indicaL.	Gliricidia sepium (Jacq.) Kunth ex Walp	Croton conduplicatus Kunth.
	A. occidentale L.	Opuntia cochenillifera (L.) Mill.	Pseudobombax marginatum (A.St.-Hil. Juss. & Cambess.) A.Robyns.
	Samanea saman (Jacq.) Merr.	Anacardium occidentale L.	Amburana cearensis A.C. Smith:
	Mimosa caesalpiniifolia Benth.	Mimosa caesalpiniifolia Benth.
	Citrus reticulatBlanco	Leucaena leucocephala (Lam.) de Wit
	Talisia esculenta (Cambess.) Radlk.	Hymenaea courbaril L.:
	Euphorbia heterophylla L.
	Handroanthus albus (Cham.) Mattos
	Ananas comosus (L.) Merr.
	A. squamosa L.
	O. cochenillifera (L.) Mill.:
7°55′03.6′′S 38°02′53.4′′W	7°55′06.0′′S 38°02′54.4′′W	7°55′'05.0′′S 38°02′52.2′′W	7°54′54.2′′S 38°03′00.2′′W
Zea mays L.;	A. squamosa L.	Gliricidia sepium (Jacq.) Kunth ex Walp	Commiphora leptophloeos (Mart.) J.B. Gillett
Opuntia cochenillifera (L.) Mill.:	Anacardium occidentale L.	Samanea saman(Jacq.) Merr.	Schinus terebinthifolius Raddi
	Mimosa caesalpiniifolia Benth.	Leucaena leucocephala (Lam.) de Wit	Aspidosperma carapanauba Pichon:
	Opuntia cochenillifera (L.) Mill.	Eugenia uniflora L.:
	Morus alba L.
	Citrus sinensis L. Osbeck.
	Malpighia punicifolia L.
	Copernicia prunifera (Miller) H. E Moore
7°55′03.3′′S 38°02′52.7′′W	7°55′04.9′′S 38°02′54.7′′W	7°55′05.0′′S 38°02′51.3′′W	7°54′53.7′′S 38°03′01.1′′W

The soil organic matter in agroecological polycultures originates from plants, pruning and post-harvest residues from the agroecosystem, and organic waste from animals that frequent the area.

According to the Köppen classification (Köppen and Geiger, 1928), this semi-arid region has a BSh climate (warm semi-arid climate). The recorded rainfall was 15.8 mm in July 2019, 171.9 mm in February 2020, and 23.0 mm in July 2020 (AccuWeather, 2022).

Soil sampling and fungal isolation

Soil samples were collected in July 2019, February 2020, and July 2020 according to the methods of Costa et al. (2012), with some adaptations. In each area (COP, AFS8, and AFS24), three equidistant plots (according to area size) were marked, totaling three sampling plots/area. In the plots, 3 soil subsamples (5 cm deep, which corresponded to the organic layer of the soil) were collected and combined into one composite sample (see the modified method, Costa et al., 2012). The samples were stored in marked plastic bags and transported to the Laboratório de Fungos Fitopatogênicos e Biocontroladores, Departamento de Micologia, Universidade Federal de Pernambuco (UFPE). To isolate filamentous fungi from the soil, serial dilution methods were used (Alves et al., 2021); 1 mL of the third dilution was transferred to Petri dishes with Sabouraud agar media and chloramphenicol (170 mg mL^˗1). Successive subcultures were prepared until axenic cultures were obtained in oatmeal agar media (Crous et al., 2021). Among the morphologies of filamentous fungi isolated from three different sustainable agroecosystems at and one fragment of the Brazilian Caatinga in July 2019, February 2020, and July 2020, fusarioid and non-fusarioid fungi were identified. Fusarioid fungi were selected and purified by single conidia subculturing. Morphological characterization was performed according to the physical and chemical criteria of Crous et al. (2021).

Identification of fusarioid fungi in soil

DNA extraction of fusarioid fungi was performed according to the protocols of the DNA Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA). To obtain the DNA sequences of the tef1 gene, PCR was performed using the primers EF1 and EF2 (O’Donnell et al., 1998) and the cycling parameters described by Santos et al. (2019). The resulting products were purified using the Exosap Illustrative enzyme ExoProStar™ 1-Step (GE Healthcare Life Sciences, Piscataway, New Jersey, USA) and sequenced using the multi-user sequencing and gene expression platform at UFPE. Electropherograms were analyzed using Sequencer 4.7 software (Gene Codes, Ann Arbor, Michigan, USA), from which consensus nucleotide sequences were obtained and exported as a FASTA file. Using these sequences, BLAST searches were conducted using the National Center for Biotechnology Information (NCBI) database to determine the matching sequences and species complexes.

The generated sequences were aligned with the reference sequences (preferably ex-type) from Crous et al. (2021) and Yilmaz et al. (2021), which were deposited in the NCBI database under the code listed in the Supplementary Material (^{Table 1S} ). The alignments were performed using MAFFT v.7 (Katoh et al., 2005) and manually optimized using MEGA v. 6.06 (Tamura et al., 2011). The most acceptable substitution model was determined using MrModeltest 2.3 (Nylander, 2004). The phylogenetic tree was constructed via the maximum likelihood method using RAxML-HPC v. 8.2.8 (Stamatakis, 2014) with 1.000 bootstrap fast inferences from the CIPRES Science Gateway (http://www.phylo.org/) (Miller et al., 2010). Trees were visualized using FigTree v.1.4.3 (Rambaut, 2009) and edited using Inkscape (2020). The sequences generated in this study were deposited in the NCBI database. The phylogenies in Figures 3, 4, and 5 are sequences of only one phylogeny, divided for better visualization of the strain’s position, Geejayessia staphylaea CBS 125482 was used as an outgroup to root the phylogenetic tree. The best branch support of the phylogenies was the maximum likehood ML analysis.

Distributions of Fusarium annulatum, F. verticillioides, F. lacertarum, and Neocosmospora vasinfecta in agroecosystems and environments in Brazil

In this study, the distribution of the species identified within Brazil was determined by an extensive search of the literature available in the Web of Science, Google Scholar, Flora do Brasil, Species Link, Global Biodiversity Information Facility (GBIF), and NCBI databases. Information from websites, dissertations, and thesis were excluded. Taxa identified only as Fusarium spp. were not used in this study. Only papers on agricultural research or native areas were included in the survey. Keywords used were Fusarium annulatum Brazil, Fusarium annulatum northeast, Fusarium verticillioides Brazil, Fusarium verticillioides northeast, Fusarium lacertarum Brazil, Fusarium lacertarum northeast, Neocosmospora vasinfecta Brazil, and Neocosmospora vasinfecta northeast. The old names for these fungi (FIESC 4 for Fusarium lacertarum, and Fusarium proliferatum for F. annulatum) were also included in the survey and are presented in Supplementary Material (^{Table 2S} ) with the names actualized according to the research area. The Index Fungorum, Mycobank, and species lists from Crous et al. (2021) and Yilmaz et al. (2021) were used for validation and verifying the synonymies of the names.

Results

Fifteen specimens of fusarioid fungi were identified from 150 specimens of filamentous fungi [Penicillium (52 specimens), Aspergillus (47), Trichoderma (10), Sterile mycelium (12), Rhizopus (4), Purpureocillium (3), Demacia fungus (3), Mucor (3), and Solitary conidiophores (1)], obtained from soil from three different sustainable agroecosystems and one fragment of the Brazilian Caatinga.

Four species were identified in two fusarioid genera: three in Fusarium and one in Neocosmospora. Nine isolates were grouped in the clade of F. verticillioides (URM 8502, URM 8496, URM 8528, URM 8497, URM 8498, URM 8499, URM 8500, URM 8501, URM 8503), one in the clade of F. annulatum (URM 8495) into the F. fujikuroi species complex (FFSC) (Figure 3), one in the clade of F. lacertarum (URM 8529) into the F. incarnatum-equiseti species complex (FIESC) (Figure 4), and one in the clade of Neocosmospora vasinfecta (URM 8504) (Figure 5). Images of plates of each species are shown in Figure 6.

Figure 3.
Maximum likelihood (ML) consensus tree based on translation elongation factor 1-α gene region (tef1) with branch support of ML analysis representing members of the F. fujikuroi species complex (FFSC). Sequences of the strains identified in this study are indicated in bold. Geejayessia staphylaea CBS 125482 was used as the outgroup.

Figure 4.
Maximum likelihood (ML) consensus tree based on translation elongation factor 1-α gene region (tef1) with branch support of ML analysis representing members of the F. incarnatum-equiseti species complex. Sequences of the strains identified in this study are indicated in bold. Geejayessia staphylaea CBS 125482 was used as the outgroup.

Figure 5.
Maximum likelihood (ML) consensus tree based on translation elongation factor 1-α gene region (tef1) with branch support of ML analysis representing members of the Neocosmospora. Sequences of the strains identified in this study are indicated in bold. Geejayessia staphylaea CBS 125482 was used as the outgroup.

Figure 6.
Fusarioid fungi isolated from different land use in the Volta do Enjeitado site, in rural Triunfo, Pernambuco, Brazil. A: From left to right: verse colonies of Fusarium verticillioides, F. annulatum, F. lacertarum and Neocosmospora vasinfecta on SNA media. B-C: Conidiophore and conidia of F. verticillioides, respectively. D-E: Conidiophore and conidia of F. annulatum, respectively. F-G: Conidiophores and conidia of F. lacertarum, respectively. H-J: Conidiophore and conidia of N. vasinfecta. Bars of scale: G, I = 10 μm; C, D, F = 15 μm; E, H, J = 20 μm; B = 25 μm.

In the soil samples obtained in July 2019 (C1), 11 specimens (URM) of F. verticillioides were isolated: three in COP (URM 8500, URM 8502, URM 8503), five isolates in AFS8 (URM 8496, URM 8497, URM 8498, URM 8499, URM 8528), two in AFS24 (URM 8500, URM 8501), and two in CA (URM 8502, URM 8503). In the soil sample obtained in February 2020 (C2), one specimen of F. annulatum in AFS24 (URM 8495) was isolated, and in the soil sample obtained in February 2021 (C3), one specimen of F. lacertarum in AFS24 (URM 8529) and N. vasinfecta in AFS24 (URM 8504) were isolated (Table 2).

Table 2.
Fusarioid fungal strains from the soils of the 15 year old consortium of plants (COP), from the 8 year old agroforestry system (AFS8), 24 year old agroforestry system (AFS24) and from the Caatinga forest fragment (CA) per sampling plots in the Volta do Enjeitado site, in rural Triunfo, Pernambuco, Brazil in July 2019 (C1), February 2020 (C2), and in July 2020 (C3).

Species	Strain	Period of collect	Area of soil sample	GenBank code
Fusarium verticillioides	URM 8496	C1	AFS8	OQ758018
	URM 8528	C1	AFS8	OQ758021
	URM 8497	C1	AFS8	OQ758023
	URM 8498	C1	AFS8	OQ758019
	URM 8499	C1	AFS8	OQ758020
	URM 8500	C1	COP; AFS24	OQ758015
	URM 8501	C1	AFS24	OQ758024
	URM 8502	C1	COP, CA	OQ758016
	URM 8503	C1	COP; CA	OQ758017
Fusarium annulatum	URM 8495	C2	AFS24	OQ758014
Fusarium lacertarum	URM 8529	C3	AFS24	OQ758013
Neocosmospora vasinfecta	URM 8504	C3	AFS24	OQ758012

The distributions of these species in Brazil are represented in Figure 7, and more details about the culture collection specimens code and district localization of the isolate of specimens are provided in ^{Table 2S} .

Figure 7.
Distribution in Brazil states and respective substrates and hosts of fusarioid fungi species isolated from soil in agroecological polycultures and tropical dry forest (fragment of the Brazilian Caatinga) of rural Triunfo. A: Distribution and substrates and hosts of Fusarium verticillioides. B: Distribution and substrates and hosts of F. annulatum. C: Distribution and substrates and hosts of F. lacertarum. D: Distribution and substrates and hosts of Neocosmospora vasinfecta.

Fusarium verticillioides was related in Brazil in 23 studies were found in the Web of Science, nine in the GBIF, and eight in the NCBI databases (^{Table 2 S} ). Of the 23 studies found in the Web of Science database, 17 addressed the pathogenic action of the species in cultivated corn and one addressed its pathogenic action in corn and rice (O. sativa L.). Other studies have also reported the pathogenic action of F. verticillioides in cultivated crops, such as sorghum [Sorghum bicolor (L.) Moench] and pineapple (Ananas comosus L.), and as a contaminant of the seeds of guajuvira (Patagonula americana L.) (Figure 7). There are also two records of the biotechnological application of F. verticillioides in cellulase production on various substrates. Of the nine studies found in the GBIF, three examined corn and one each considered Bauhinia forficata Link, Plantago major L., buriti chestnut (Mauritia flexuosa L), Phaseolus lunatus L., and cow dung. Of the eight isolates found in NCBI, four were related to phytopathogenic action in maize, three were associated with P. lunatus L., Nopalea cochenillifera L., and Urochloa sp. (um), and two were related to the biological control of insects (Figure 7).

Fusarium annulatum was found to be an endophyte of Cavanillesia arborea in the state of Minas Gerais, in the municipality of Manga, a region containing fragment of the Brazilian Caatinga (^{Table 2S} ).

Fusarium lacertarum was found in Brazil causing diseases in Casuarina equisetifolia L., N. cochenillifera L., and rice. There are also reports of its use in controlling the worm, Scrobipalpuloides absoluta [Lepidoptera: Gelechiidae] (^{Table 2S} ) (Figure 7).

Neocosmospora vasinfecta was found in Brazil in soil, plants, and animal dung (^{Table 2 S} ); additionally, it causes rot in Cucumis spp. (Figure 7).

Discussion

The low occurrence of fusarioid fungi (15 specimens) compared with non-fusarioid fungi (150 specimens) indicates that the ecological management of the soil contributes to a decrease in the population of fusarioid fungi, which are known to be phytopathogenic in agricultural environments. Fusarioid fungi occurred more commonly in the AFSs, possibly because of the larger number of seeds and other types of vegetable materials introduced in the system, compared to those in the COP, which can act as a source of fungal inocula. In the fragment of the Brazilian Caatinga, the vegetation at the collection points was native and consisted of plants that were not commonly associated with Fusarium spp. Furthermore, throughout the long cultivation period at AFS24, many plants participated in the agroecological transition process (Alves et al., 2021, Barreto et al., 2021). This may have influenced the introduction and maintenance of these fungi in the environment.

Fusarium verticillioides (Figure 6) and F. annulatum (Figure 6) belong to the F. fujikuroi species complex. This species complex is among the largest and most studied complexes within Fusarium across several ecosystems (Sandoval Denis et al., 2018; Al-Hatmi et al., 2019; Yilmaz et al., 2021). It comprises mycotoxin producers and species known to cause diseases in grains, such as corn (Z. mays L.) cob and stalk rot and bakanae disease (in rice, Oryza sativa L.), among others (Choi et al., 2018; Barreto et al., 2021).

Fusarium verticillioides (Figure 6) is commonly found in subtropical and tropical regions (Leyva-Madrigal et al., 2015). The species in these isolates are commonly found in tropical and temperate regions, with more than 200 species reported as host plants (Yilmaz et al., 2021).

Fusarium annulatum (Figure 6) is a pathogen of several plants of economic interest, such as rice, sorghum, mango (Mangifera indica L.), and asparagus (Asparagus officinalis L.) (Yilmaz et al., 2021), and date palm (Phoenix dactylifera L.) (Khazaal et al., 2019). In the databases used to survey the species distributions in the dry forest in the northeastern region of Brazil (rural Triunfo), there was no occurrence of this species in other hosts or substrates; hence, URM 8495 was the first record for Pernambuco and the first for northeastern Brazil.

Fusarium lacertarum (Figure 6) belongs to the species complex of F. incarnatum-equiseti. Species of this complex are cosmopolitan and have been isolated from many biological sources, such as soil, insects, and plants (Xia et al., 2019; Santos et al., 2020).

Neocosmospora, previously known as Fusarium solani (Sandoval-Denis et al., 2018, 2019), is a ubiquitous genus commonly found in soil, plant residues, and live plants. Neocosmospora is frequently associated with root and vascular system diseases in plants and includes important phytopathogenic species (Sandoval-Denis et al., 2019). Neocosmospora vasinfecta is a registered pathogen of peanut roots (Arachis hypogaea L.) in northern China and peanuts in Vietnam, Australia, South Africa, Taiwan, and Guine (Baard and van Wyk, 1985; Huang et al., 1992; Fuhlbohm et al., 2007; Dau et al., 2010; Sun et al., 2012; Lombard et al., 2015). It is also registered in other plants (Manikandan et al., 2011) and is commonly isolated from soil (Sandoval-Denis et al., 2019).

Some crops of economic importance are cultivated in northeast Brazil, including maize, cassava, Cucumis spp., pineapple, forage palm, and Citrus spp. (Nascimento et al., 2018; Santiago et al., 2018; Silva et al., 2020; Viana et al., 2020; Barbosa et al., 2021; Nascimento et al., 2021). The sustainable agricultural management of these crops consists of plant diversification, frequent pruning of arboreal plants, crop rotation for herbaceous species, mulching to protect the soil, mitigating the use of chemical inputs in the system, keeping the soil healthy with the necessary concentrations of micro- and macronutrients, and maintaining a dynamic balance of niches that favors the occurrence of natural pest and plant disease controllers (Alves et al., 2021; Barbosa et al., 2021; Lima et al., 2021). In contrast, agroecosystems that practice conventional agricultural management modify the ecology of the agricultural environment and potentiate the pathogenic action of certain soil-colonizing microorganisms, such as fusarioid fungi, thereby affecting the productivity and biological value of their crops (Nascimento et al., 2018).

The fusarioid fungi identified in this study are potential plant pathogens (Nascimento et al., 2018; Avila et al., 2019; Nicolli et al., 2020; Viana et al., 2020). These fungi naturally colonize the soil and host plants. Moreover, members of some genera, such as Neocosmospora, can produce resistant spores (chlamydospores), which remain dormant in the environment for a long time, and are reactivated under favorable physiological conditions (Crous et al., 2021).

Sustainable agricultural management can control populations, and consequently, the pathogenicity of fusarioid fungi. In melons, a relationship has been found between soil management (direct or conventional planting) and the incidence of root rot caused by N. vasinfecta. The incidence of the disease was lower in soils with direct planting and a crop rotation system with crotalaria, millet, and spontaneous vegetation (Nascimento et al., 2018).

Another example showing that soil management influences microorganisms in the environment was described by da Silva et al. (2021). They sampled the root microbial population of a consortium of Vigna unguiculata, V. radiata, and V. mungo in a preserved area of the Caatinga forest. They isolated the fungi that caused root rot in these plants, such as F. verticillioides, and bacteria with biocontrol potential. Their tests showed that 24 bacteria of the genera Agrobacterium sp., Bradyrhizobium sp., Bacillus sp., Enterobacter sp., Pseudomonas sp., Paraburkholderia sp., and Rhizobium sp. inhibited the harmful effects of Macrophomina sp. and Fusarium sp., increasing the germination and growth of potted plants.

Research on fusarioid fungi has focused on assessing potentially pathogenic species because of their economic importance. These studies obtained microorganisms from crop areas of commercial importance where, in most cases, they caused plant diseases (Leslie and Summerell, 2011). However, studies on fungi isolated from different environments, including areas of agricultural subsistence, showed that when these fungi were isolated from environments with diverse plant substrates, their pathogenic responses were suppressed. Furthermore, the host was often also in the same environment but did not have any disease (Leslie and Summerell, 2011; Alves et al., 2021). The biogeographic success of cosmopolitan fusarioid fungi resulted naturally or from the influence of human actions. The custom of implementing agricultural monoculture systems for many years has enabled these species, which are currently considered pathogens, to develop successful evolutionary strategies, such as genetic diversification, making it difficult to control them in the field. When their hosts had no commercial or export value, these fungal species were subjected to balanced environments in which biotic and abiotic conditions suppressed their pathogenicity (Summerell et al., 2010).

Subsistence and conventional agriculture differ significantly in terms of geographic size and profits. Subsistence agriculture occupies a smaller area than commercial agriculture (approximately 2 ha is considered a common size for areas under subsistence agriculture). Profits for conventional agriculture tend to be larger, as it involves the cultivation of only one crop (monoculture) (Leslie and Summerell, 2011). However, subsistence agriculture uses a plant substrate that does not favor the pathogenicity of fusarioid fungi. These agricultural crops are generally located near areas of native plants and have a diversified plant cultivation substrate (Leslie and Summerell, 2011; Arias Mota and Abarca, 2020).

When comparing the results of the survey of fusarioid fungi isolated from ecologically managed agroecosystems in rural Triunfo to the distributions and status of these fungi in various regions of Brazil (Figure 7), it was noted that these microorganisms appear to prefer the main commodities in the country (grain-producing plant species). Other studies have shown that these fungi occur in natural and sustainably managed ecosystems, without causing plant diseases (Crous et al., 2021; Yilmaz et al., 2021).

Conclusion

The specimen isolation of fusarioid fungi in sustainable agricultural environments and fragment of the Brazilian Caatinga in rural Triunfo (Brazil) and the comparison of the behavior of these species in other agricultural areas and natural environments in Brazil, indicate that sustainable agricultural practices, such as crop diversification, rotation, and reduction of chemical inputs, can suppress the pathogenicity of fusarioid fungi. It also emphasizes the importance of maintaining different niches in the ecosystem, which can favor the occurrence of other fungi that naturally control pests and diseases.

Acknowledgements

To Fundação de Amparo a Ciência em Pernambuco (FACEPE) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for supporting research (grant numbers 406651/2021-3), Sabiá – Centro de Desenvolvimento Agroecológico and the farmer Antônio Alves de Queiroz for partnership with the research.

References

• AccuWeather. 2022. AccuWeather Inc. https://www.accuweather.com/ 21 Jun. 2022.
  » https://www.accuweather.com/
• Al-Hatmi AMS, Sandoval-Denis M, Nabet C et al 2019. Fusarium volatile, a new potential pathogen from a human respiratory sample. Fungal Systematics and Evolution 4: 171-181. doi: 10.3114/fuse.2019.04.09.
  » https://doi.org/10.3114/fuse.2019.04.09.
• Alves AL, Santos ACS, de Mattos JLS et al 2021. Diversity of filamentous fungi communities in the soils of agroecological crop polycultures and the Atlantic Rain Forest. Archives of Agronomy and Soil Science 6: 374-386. doi: 10.1080/03650340.2021.1995717
  » https://doi.org/10.1080/03650340.2021.1995717
• Alves AL, Santos ACS, Melo RFR, Tiago PV. 2023. Black mildew fungi in polycultures from agroecological transition areas. Anais da Academia Pernambucana de Ciência Agrônoma 19: 1-12.
• Arias Mota RM, Abarca GH. 2020. Diversity of soil culturable fungi in the tropical montane cloud forest of Veracruz, Mexico. Scientia Fungorum 50: e1290. doi: 10.33885/sf.2020.50.1290
  » https://doi.org/10.33885/sf.2020.50.1290
• Avila CF, Moreira GM, Nicolli CP et al 2019. Fusarium incarnatum-equiseti species complex associated with Brazilian rice: Phylogeny, morphology and toxigenic potential. International Journal of Food Microbiology 30: 108267. doi: 10.1016/j.ijfoodmicro.2019.108267
  » https://doi.org/10.1016/j.ijfoodmicro.2019.108267
• Baard SW, van Wyk PS. 1985. Neocosmospora vasinfecta pathogenic to groundnuts in South Africa. Phytophylactica 17: 49-50.
• Barbosa LFS, Santos ACS, Diniz AG et al 2021. Entomopathogenicity of fungi in combination with Ricinus communis extract for the control of Aleurocanthus woglumi Entomologia Experimentalis et Applicata 169: 838-847. doi: 10.1111/eea.13080
  » https://doi.org/10.1111/eea.13080
• Barreto GG, Santos ACS, Porcino MM et al 2021. Antagonism of Trichoderma on the control of Fusarium spp. on Phaseolus lunatus L. Acta Brasiliensis 5: 57-64. doi: 10.22571/2526-4338516
  » https://doi.org/10.22571/2526-4338516
• Choi JH, Lee S, Nah JY et al 2018. Species composition of and fumonisin production by the Fusarium fujikuroi species complex isolated from Korean cereals. International Journal of Food Microbiology 267: 62-69. doi: 10.1016/j.ijfoodmicro.2017.12.006
  » https://doi.org/10.1016/j.ijfoodmicro.2017.12.006
• Costa PMO, Souza-Motta CM, Malosso E. 2012. Diversity of filamentous fungi in different systems of land use. Agroforestry Systems 85: 195-203. doi: 10.1007/s10457-011-9446-8
  » https://doi.org/10.1007/s10457-011-9446-8
• Crous PW, Lombard L, Sandoval-Dennis M et al 2021. Fusarium: More than a node or a foot-shaped basal cell. Studies in Mycology 98: 100116. doi: 10.1016/j.simyco.2021.100116
  » https://doi.org/10.1016/j.simyco.2021.100116
• da Silva VB, Bomfim CSG, Sena PTS et al 2021. Vigna spp. root-nodules harbor potentially pathogenic fungi controlled by co-habiting bacteria. Current Microbiology 78: 1835-1845. doi: 10.1007/s00284-021-02455-3
  » https://doi.org/10.1007/s00284-021-02455-3
• Dau VT, Pham LT, Luong MT et al 2010. First report of Neocosmospora vasinfecta associated with the root rot complex of peanuts in Vietnam. Australasian Plant Disease Notes 5: 79-81. doi: 10.1071/DN10028
  » https://doi.org/10.1071/DN10028
• Fuhlbohm MF, Tatnell JR, Ryley MJ. 2007. Neocosmospora vasinfecta is pathogenic on peanut in Queensland. Australasian Plant Disease Notes 2: 3-4. doi: 10.1071/DN07002
  » https://doi.org/10.1071/DN07002
• Huang JW, Chen SS, Chung W. 1992. Neocosmospora Foot Rot of Peanut in Taiwan. Plant Pathology Bulletin 1: 203-205.
• Inkscape Project. 2020. Inkscape (Draw Freely). https://inkscape.org/ 21 Jun. 2022.
  » https://inkscape.org/
• Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
• Khazaal FAK, Ameen MKM, Ali AH. 2019. Pathogenic fungi accompanied with sudden decline syndrome (wilting disease) of date palm tree (Phonix dactylifera L.). Basrah Journal of Science 37: 376-397.
• Köppen W, Geiger R. 1928. Klimate der Erde. Gotha, Justus Perthes.
• Leslie J, Summerell B. 2011. In search of new Fusarium species. Plant Breeding and Seed Science 63: 93-101.
• Leyva-Madrigal KY, Corona CPL, Sánchez MAA et al 2015. Fusarium species from the Fusarium fujikuroi species complex involved in mixed infections of maize in Northern Sinaloa, Mexico. Journal of Phytopathology 163: 486-497. doi: 10.1111/jph.12346
  » https://doi.org/10.1111/jph.12346
• Lima EN, Oster AH, Bordallo PN, Araújo AAC, Silva DEM, Lima CS. 2021. A novel lineage in the Fusarium incarnatum-equisetispecies complex is one of the causal agents of Fusarium rot on melon fruits in Northeast Brazil. Plant Pathology 70: 133-143. doi: 10.1111/ppa.13271
  » https://doi.org/10.1111/ppa.13271
• Lombard L, van der Merwe NA, Groenewald JZ, Crous PW. 2015. Generic concepts in Nectriaceae. Studies in Mycology 80: 189-245. doi: 10.1016/j.simyco.2014.12.002
  » https://doi.org/10.1016/j.simyco.2014.12.002
• Manikandan P, Vágvölgyi C, Narendran V, Panneer Selvam K, Kredics L. 2011. Neocosmospora In: Liu D (ed.). Molecular Detection of Human Fungal Pathogens. Boca Raton, CRC Press. p. 449-458.
• Marchiori CH. 2021. Intraspecific ecological relationships harmonious and inharmonious of parasitoids Class Insect Order Hymenoptera and a review. Open Access Research Journal of Multidisciplinary Studies 2: 13-30.
• Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), 14 November 2010, New Orleans. p. 1-8.
• Nascimento PGML, Ambrósio MMQ, Freitas FCL et al 2018. Incidence of root rot of musk melon in different soil management practices. European Journal of Plant Pathology 152: 433-446. doi: 10.1007/s10658-018-1488-6
  » https://doi.org/10.1007/s10658-018-1488-6
• Nascimento RDC, Cavalcanti MIP, Correia AJ et al 2021. Maize-associated bacteria from the Brazilian semi-arid region boost plant growth and grain yield. Symbiosis 83: 347-359. doi: 10.1007/s13199-021-00755-7
  » https://doi.org/10.1007/s13199-021-00755-7
• Nicolli CP, Haidukowski M, Suscaet A et al 2020. Fusarium fujikuroi species complex in Brazilian rice: Unveiling increased phylogenetic diversity and toxigenic potential. International Journal of Food Microbiology 330: 108667. doi: 10.1016/j.ijfoodmicro.2020.108667
  » https://doi.org/10.1016/j.ijfoodmicro.2020.108667
• Nylander JAA. MrModelTest version 2. 2004. Evolutionary Biology Centre, Uppsala University, Sweden. https://github.com/nylander/MrModeltest2/ 20 Dec. 2020.
  » https://github.com/nylander/MrModeltest2/
• O’Donnell K, Kistler HC, Cigelnik E, Ploetz RC. 1998. Multiple evolutionary origins of the fungus causing Panama disease of banana: Concordant evidence from nuclear and mitochondrial gene genealogies. Proceedings of the National Academy of Sciences of the United States of America 95: 2044-2049.
• O’Donnell K, McCormick SP, Busman M et al 2018. Marasas et al 1984 “Toxigenic Fusarium Species: identity and Mycotoxicology” revisited. Mycologia 110: 1058-1080. doi: 10.1080/00275514.2018.1519773
  » https://doi.org/10.1080/00275514.2018.1519773
• Poletto T, Marciel CG, Muniz MFB et al 2015. First report of Fusarium lacertarum causing damping-off in Casuarina equisetifolia in Brazil. Plant Disease 99: 7. doi: 10.1094/PDIS-12-14-1272-PDN.
  » https://doi.org/10.1094/PDIS-12-14-1272-PDN.
• Rambaut A. 2009. FigTree 1.3.1. Software. Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk/software/
  » http://tree.bio.ed.ac.uk/software/
• Ronquist F, Teslenko M, van der Market P et al 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
• Sandoval-Denis M, Guarnaccia V, Polizzi G, Crous PW. 2018. Symptomatic Citrus trees reveal a new pathogenic lineage in Fusarium and two new Neocosmospora species. Persoonia 40: 25. doi: 10.3767/persoonia.2018.40.01
  » https://doi.org/10.3767/persoonia.2018.40.01
• Sandoval-Denis M, Lombard L, Crous PW. 2019. Back to the roots: A reappraisal of Neocosmospora Persoonia 43: 90-185. doi: 10.3767/persoonia.2019.43.04
  » https://doi.org/10.3767/persoonia.2019.43.04
• Santiago MF, Santos AMG, Inácio CP et al 2018. First report of Fusarium lacertarum causing cladode rot in Nopalea cochenellifera in Brazil. Journal of Plant Pathology 100: 611. doi: 10.1007/s42161-018-0120-0
  » https://doi.org/10.1007/s42161-018-0120-0
• Santos ACDS, Trindade JVC, Lima CS, Barbosa RDN, da Costa AF, Tiago PV, de Oliveira NT. 2019. Morphology, phylogeny, and sexual stage of Fusarium caatingaense and Fusarium pernambucanum, new species of the Fusarium incarnatum-equiseti species complex associated with insects in Brazil. Mycologia 111: 244-259. doi: 10.1080/00275514.2019.1573047
  » https://doi.org/10.1080/00275514.2019.1573047
• Santos ACDS, Diniz AG, Tiago PV, Oliveira NTD. 2020. Entomopathogenic Fusarium species: A review of their potential for the biological control of insects, implications and prospects. Fungal Biology Reviews 34: 41-57. doi: 10.1016/j.fbr.2019.12.002
  » https://doi.org/10.1016/j.fbr.2019.12.002
• Silva JMC, Barbosa LCF. 2017. Impact of human activities on the caatinga. In: Silva JMC, Leal IR, Tabarelli M (eds.) Caatinga. Cham, Springer. doi: 10.1007/978-3-319-256 68339-3_13
  » https://doi.org/10.1007/978-3-319-256 68339-3_13
• Silva MJS, Silva GCS, Viana Neto JD, Infante NB, Feijó FM, Assunção IP, Lima GSA. 2020. Fusarium spp. associadas a mancha-marrom da palma forrageira miúda. Caderno Verde de Agroecologia e Desenvolvimento Sustentável 10: f5.
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313. doi: 10.1093/bioinformatics/btu033
  » https://doi.org/10.1093/bioinformatics/btu033
• Summerell BA. 2019. Resolving Fusarium: Current status of the genus. Annual Review of Phytopathology 57: 323-339. doi: 10.1146/annurev-phyto-082718-100204
  » https://doi.org/10.1146/annurev-phyto-082718-100204
• Summerell BA, Laurence MH, Liew ECY, Leslie JF. 2010. Biogeography and phylogeography of Fusarium: A review. Fungal Diversity 44: 3-13. doi: 10.1007/s13225-010-0060-2
  » https://doi.org/10.1007/s13225-010-0060-2
• Sun WM, Feng LN, Guo W, Liu DQ, Li YN, Ran LX. 2012. First report of peanut pod rot caused by Neocosmospora vasinfecta in Northern China. Plant Disease 96: 455. doi: 10.1094/PDIS-03-11-0240
  » https://doi.org/10.1094/PDIS-03-11-0240
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739. doi: 10.1093/molbev/msr121
  » https://doi.org/10.1093/molbev/msr121
• Viana EDS, Sasaki FFC, Reis RC, Junghans DT, Guedes ISA, Souza EG. 2020. Quality of fusarioid-resistant pineapple frf-632, harvested at different maturity stages. Revista Caatinga 33: 541-549. doi: 10.1590/1983-21252020v33n226rc
  » https://doi.org/10.1590/1983-21252020v33n226rc
• Xia JW, Sandoval-Denis M, Crous PW, Zhang XG, Lombard L. 2019. Numbers to names - restyling the Fusarium incarnatum-equiseti species complex. Persoonia 43: 186-221. doi: 10.3767/persoonia.2019.43.05
  » https://doi.org/10.3767/persoonia.2019.43.05
• Yergeau E, Labour K, Hamel C, Vujanovic V, Nakano-Hylander A, Jeannotte R, St-Arnaud M. 2010. Patterns of Fusarium community structure and abundance in relation to spatial, abiotic and biotic factors in soil. FEMS Microbiology Ecology 71: 34-42. doi: 10.1111/j.1574-6941.2009.00777.x
  » https://doi.org/10.1111/j.1574-6941.2009.00777.x
• Yilmaz N, Sandoval-Denis M, Lombard L, Visagie CM, Wingfield BD, Crous PW. 2021. Redefining species limits in the Fusarium fujikuroi species complex. Persoonia 46: 129-162. doi: 10.3767/persoonia.2021.46.05
  » https://doi.org/10.3767/persoonia.2021.46.05

• Research Data
  The raw data of this research are assured by the corresponding author and will be shared.

Supplementary Material

The following online material is available for this article:

Table S1 - Sequences of strains obtained by NCBI (National Center for Biotechnology Information) used for phylogenetic analyses of fusarioid fungi of sustainable crops cultures and fragment of the Brazilian Caatinga. Table S2 - Register of Fusarium verticillioides, F. annulatum, F. lacertarum and Neocosmospora vasinfecta in Brazil based on data of agriculture, according databases Web Of Science, Google Scholar, Flora do Brasil, Species Link, Global Biodiversity Information Facility (GBIF) and NCBI, and they ecological relationship with substrate/ host of origin.

Edited by

• Editor-in-Chief:
  Thaís Elias Almeida

• Associate Editor:
  Tatiana Baptista Gibertoni

Data availability

The raw data of this research are assured by the corresponding author and will be shared.

Publication Dates

• Publication in this collection
  12 Aug 2024
• Date of issue
  2024

History

• Received
  12 May 2023
• Accepted
  06 Dec 2023