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Review

Microbes' role in environmental pollution and remediation: a bioeconomy focus approach

  • Bioremediation stands as a promising solution amid the escalating challenges posed by environmental pollution. Over the past 25 years, the influx of synthetic chemicals and hazardous contaminants into ecosystems has required innovative approaches for mitigation and restoration. The resilience of these compounds stems from their non-natural existence, distressing both human and environmental health. Microbes take center stage in this scenario, demonstrating their ability of biodegradation to catalyze environmental remediation. Currently, the scientific community supports a straight connection between biorefinery and bioremediation concepts to encourage circular bio/economy practices. This review aimed to give a pre-overview of the state of the art regarding the main microorganisms employed in bioremediation processes and the different bioremediation approaches applied. Moreover, focus has been given to the implementation of bioremediation as a novel approach to agro-industrial waste management, highlighting how it is possible to reduce environmental pollution while still obtaining value-added products with commercial value, meeting the goals of a circular bioeconomy. The main drawbacks and challenges regarding the feasibility of bioremediation were also reported.

    Citation: Giuseppe Maglione, Paola Zinno, Alessia Tropea, Cassamo U. Mussagy, Laurent Dufossé, Daniele Giuffrida, Alice Mondello. Microbes' role in environmental pollution and remediation: a bioeconomy focus approach[J]. AIMS Microbiology, 2024, 10(3): 723-755. doi: 10.3934/microbiol.2024033

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  • Bioremediation stands as a promising solution amid the escalating challenges posed by environmental pollution. Over the past 25 years, the influx of synthetic chemicals and hazardous contaminants into ecosystems has required innovative approaches for mitigation and restoration. The resilience of these compounds stems from their non-natural existence, distressing both human and environmental health. Microbes take center stage in this scenario, demonstrating their ability of biodegradation to catalyze environmental remediation. Currently, the scientific community supports a straight connection between biorefinery and bioremediation concepts to encourage circular bio/economy practices. This review aimed to give a pre-overview of the state of the art regarding the main microorganisms employed in bioremediation processes and the different bioremediation approaches applied. Moreover, focus has been given to the implementation of bioremediation as a novel approach to agro-industrial waste management, highlighting how it is possible to reduce environmental pollution while still obtaining value-added products with commercial value, meeting the goals of a circular bioeconomy. The main drawbacks and challenges regarding the feasibility of bioremediation were also reported.



    In theoretical chemistry, the topological index of a graph, also called molecular structure descriptor, is a real number related to a structural graph of a molecule, and is often used to predict the physico-chemical properties and biological activities of molecules. A large number of molecular structure descriptors have been conceived and several of them have found applications in quantitative structure-activity and structure-property relationships (QSAR/QSPR) studies. In particular, degree-based topological indices and distance-based topological indices are the most important molecular structure descriptors that play an important role in QSAR/QSPR.

    Throughout in this paper, G is a simple connected undirected graph with the vertex set V(G) and edge set E(G). For u,vV(G), dv is the degree of vertex v in G and d(u,v) is the distance between vertices u and v in G. As a molecular descriptor, the Wiener index, introduced by Wiener [1] in 1947, is considered as one of the most used topological indexes with high correlation with many physical and chemical indices of molecular compounds. The Wiener index equals the sum of distances between all pairs of vertices of a graph G, that is,

    W(G)={u,v}V(G)d(u,v).

    In 1989, the Schultz index [2] of a chemical graph G was put forward as a topological index of alkanes. It is defined as

    S(G)={u,v}V(G)(du+dv)d(u,v).

    The proposal of this index has opened up the research on the degree-distance-type index. Plavšić et al. [3] showed that the Wiener index and the Schultz index are highly intercorrelated topological indices. For arbitrary catacondensed benzenoid graphs, Dobrynin [4] proved that the Schultz index has the same discriminating power with the Wiener index. So, it is both significant and interesting to study the Schultz index for some given class of graphs (or network), no matter whether they are molecular graphs or not.

    In 1994, Gutman [5] proposed the Schultz index of the second kind, often called the Gutman index, and defined it as

    Gut(G)={u,v}V(G)dudvd(u,v).

    Bounds of this index have been extensively studied using mathematical methods; see [6]. Moreover, for a tree T on n vertices, the Gutman index and Wiener index are closely related by

    Gut(T)=4W(T)(n1)(2n1).

    In 2021, from a geometric perspective (degree radius), Gutman [7] introduced a novel degree-based topological index called the Sombor index, which is defined as

    SO(G)=uvE(G)d2u+d2v.

    Note that the Sombor index is the sum of Euclidean distances of the degrees of the two vertices of each edge in the graph. This index is widely studied in mathematics and chemistry; see [8].

    Inspired by the above research, we propose a new topological index called the Sombor-Wiener (SW) index, and define it as

    SW(G)={u,v}V(G)d2u+d2vd(u,v).

    The new index can be regarded as the sum of the product of degree radius and distance between any two vertices in the graph, which is a novel version of the distance-based topological index.

    Naturally, we define a general topological index DWW(G) of a graph G contributed by the degree weights of all vertices as

    DWW(G)={u,v}V(G)f(du,dv)d(u,v),

    where f(du,dv) is a real function of du and dv with

    f(du,dv)0andf(du,dv)=f(dv,du).

    Clearly, the general topological index, called the degree-weighted Wiener index, is the generalization of the Schultz index, the Gutman index, and the SW index.

    In this paper, we study the basic properties of the SW index, and the linear regression analysis of the SW index, with respect to acentric factor of octane isomers. In addition, we give the calculation formula of degree-weighted Wiener index for generalized Bethe trees. Our results generalize some known formulae on the Schultz index and Gutman index.

    Theorem 2.1. Let G be a connected graph with n vertices.

    (i) If G=Pn, then

    SW(G)=(n1)(2(n25n+9)3+5(n2)).

    (ii) If G is r-regular, then

    SW(G)=2rW(G).

    Moreover, if G=Kn, then

    SW(G)=2n(n1)22.

    If G=Cn, then

    SW(G)={2n34,if n is even;2n(n21)4, if n is odd.

    (iii) If G=Kn1,n2, then

    SW(G)=n1n2[n21+n22+2(n1+n2)22].

    In particular, if G=K1,n1, then

    SW(G)=(n1)(n22n+2+2n22).

    Proof. (i) If G=Pn, then

    SW(G)={u,v}V(G)d2u+d2vd(u,v)=5(1+2++n2)+2(n1)+22(1+2++n3)+5(n2)++22+25+5=5(n1)(n2)2+2(n1)+22(1+3++(n3)(n2)2)+5(1+2++n2)=2(n1)+5(n1)(n2)+22(n1)(n2)(n3)6=(n1)(2(n25n+9)3+5(n2)).

    (ii) If G is r-regular, then

    SW(G)={u,v}V(G)r2+r2d(u,v)=2rW(G).

    In particular, if G=Kn, then

    SW(G)=2(n1)W(G)=2(n1)n(n1)2=2n(n1)22.

    If G is a cycle Cn, from [9], we have

    SW(G)={2n34,if   n   is even;2n(n21)4, if   n  is odd.

    (iii) If G=Kn1,n2, then

    SW(G)={u,v}V(G)d2u+d2vd(u,v)=n1n2n21+n22+2(n12)n22+n22+2(n22)n21+n21=n1n2[n21+n22+2(n1+n2)22].

    Let n1=1 and n2=n1, then

    SW(K1,n1)=(n1)(n22n+2+2n22).

    This completes the proof.

    Theorem 2.2. Let G be a connected graph with the maximum degree Δ and the minimum degree δ, then

    2δW(G)SW(G)2ΔW(G)

    with equality if, and only if, G is regular.

    Proof. By definition of SW(G), we have the proof.

    Corollary 2.3. Let G be a connected graph with n vertices, then

    2W(G)SW(G)2(n1)W(G).

    Theorem 2.4. Let G be a connected graph with the minimum degree δ, then

    12S(G)SW(G)S(G)(22)δW(G) (2.1)

    with equality (left and right) if, and only if, G is regular.

    Proof. First, we prove the left-hand side of (2.1). By Cauchy-Schwarz's inequality, we have

    SW(G)={u,v}V(G)d2u+d2vd(u,v){u,v}V(G)12(du+dv)d(u,v)=12S(G)

    with equality if, and only if, du=dv for u,vV(G), that is, G is regular.

    Second, we prove the righthand side of (2.1). For any u,vV(G) (dudv), we have

    d2u+d2vdu+(21)dv

    with equality if, and only if, du=dv. Thus,

    SW(G)={u,v}V(G)d2u+d2vd(u,v){u,v}V(G)[du+(21)dv]d(u,v){u,v}V(G)(du+dv)d(u,v){u,v}V(G)(22)δd(u,v)S(G)(22)δW(G)

    with equality if, and only if, G is regular.

    This completes the proof.

    Theorem 2.5. Let G be a connected graph with the maximum degree Δ and the minimum degree δ, then

    2ΔGut(G)SW(G)2δGut(G)

    with equality (left and right) if, and only if, G is regular.

    Proof. Note that

    d2u+d2v=dudv1d2u+1d2v,

    then we have

    SW(G)={u,v}V(G)d2u+d2vd(u,v){u,v}V(G)dudv1δ2+1δ2d(u,v)=2δ{u,v}V(G)dudvd(u,v)=2δGut(G)

    and

    SW(G)={u,v}V(G)d2u+d2vd(u,v){u,v}V(G)dudv1Δ2+1Δ2d(u,v)=2Δ{u,v}V(G)dudvd(u,v)=2ΔGut(G).

    This completes the proof.

    The generalized Bethe tree is an important graph structure that has wide applications in many fields. The investigation on topological indices of generalized Bethe trees and dendrimer trees frequently appeared in various journals. A Bethe tree Bk,d is a rooted tree at k levels whose root is on level 1 and has degree equal to d, the vertices of levels from 2 to k1 have degrees equal to d+1, and the vertices on the level k have degree equal to 1; see [10]. In 2007, Rojo [11] generalized the notion of a Bethe tree as follows: A generalized Bethe tree Bk is a rooted tree whose vertices at the same level have equal degrees. Moreover, a regular dendrimer tree Tk,d is a generalized Bethe tree of k+1 levels with each non-pendent vertex having degree d.

    Theorem 3.1. Let Bk+1 be a generalized Bethe tree of k+1 levels. If d1 denotes the degree of rooted vertex and di+1 denotes the degree of vertices on the i-th level of Bk+1 for i<1k, then

    DWW(Bk+1)=k+1l=1Al,

    where nj is the number of vertices on the j-th level of Bk+1, and

    n1=1andnj+1=d1d2dj

    for 1jk, and

    A1=kj=2nj(j1)f(d1,dj+1)+knk+1f(d1,1),Al=[2(dl12)+4(dl11)(dl1dl2dl11)++2(l1)(dl1d21)(nldl1d21)]f(dl+1,dl+1)+kj=l+1nj(jl)f(dl+1,dj+1)+(kl+1)nk+1f(dl+1,1)+(dl11)[kj=l+1nj(jl+2)f(dl+1,dj+1)+(kl+3)nk+1f(dl+1,1)]+(dl1dl2dl1)[kj=l+1nj(jl+4)f(dl+1,dj+1)+(kl+5)nk+1f(dl+1,1)]++(nldl1d2)[kj=l+1nj(j+l2)f(dl+1,dj+1)+(k+l1)nk+1f(dl+1,1)],Ak+1=f(1,1)[2(dk2)+4(dk1)(dkdk1dk1)++2k(dkd21)(nk+1dkd21)].

    Proof. Let Ai be the value of degree-weighted Wiener index of vertices on the i-th level of Bk+1, then

    DWW(Bk+1)=k+1i=1Ai.

    By definition of Bk+1, we have

    A1=n2f(d1,d2+1)+2n3f(d1,d3+1)++(k1)nkf(d1,dk+1)+knk+1f(d1,1)=kj=2nj(j1)f(d1,dj+1)+knk+1f(d1,1),A2=2(d12)f(d2+1,d2+1)+n2[d2f(d2+1,d3+1)+2d2d3f(d2+1,d4+1)++d2d3dk1(k2)f(d2+1,dk+1)+d2d3dk(k1)f(d2+1,1)+(n21)(3d2f(d2+1,d3+1)+4d2d3f(d2+1,d4+1)++d2d3dk1kf(d2+1,dk+1)+d2d3dk(k+1)f(d2+1,1))]=d1(d11)f(d2+1,d2+1)+n2[n3/d1f(d2+1,d3+1)+2n4/d1f(d2+1,d4+1)++nk/d1(k2)f(d2+1,dk+1)+nk+1/d1(k1)f(d2+1,1)+(n21)(3n3/d1f(d2+1,d3+1)+4n4/d1f(d2+1,d4+1)++knk/d1f(d2+1,dk+1)+nk+1/d1(k+1)f(d2+1,1))]=d1(d11)f(d2+1,d2+1)+n2/d1[kj=3(j2)njf(d2+1,dj+1)+(k1)nk+1f(d2+1,1)+(n21)(kj=3jnjf(d2+1,dj+1)+(k+1)nk+1f(d2+1,1))]=d1(d11)f(d2+1,d2+1)+kj=3(j2)njf(d2+1,dj+1)+(k1)nk+1f(d2+1,1)+(n21)[kj=3jnjf(d2+1,dj+1)+(k+1)nk+1f(d2+1,1)],A3=[2(d22)+4(d21)(n3d21)]f(d3+1,d3+1)+n3[d3f(d3+1,d4+1)+2d3d4f(d3+1,d5+1)++(k3)d3d4dk1f(d3+1,dk+1)+(k2)d3d4dkf(d3+1,1)+(d21)(3d3f(d3+1,d4+1)+4d3d4f(d3+1,d5+1)++(k1)d3d4dk1f(d3+1,dk+1)+kd3d4dkf(d3+1,1))+(n3d2)(5d3f(d3+1,d4+1)+6d3d4f(d3+1,d5+1)++(k+1)d3d4dk1f(d3+1,dk+1)+(k+2)d3d4dkf(d3+1,1))]=[2(d22)+4(d21)(n3d21)])f(d3+1,d3+1)+kj=4nj(j3)f(d3+1,dj+1)+(k2)nk+1f(d3+1,1)+(d21)[kj=4nj(j1)f(d3+1,dj+1)+knk+1f(d3+1,1)]+(n3d2)[kj=4nj(j+1)f(d3+1,dj+1)+nk+1(k+2)f(d3+1,1)].

    By calculating similarly to the above, for any 2lk, we have

    Al=[2(dl12)+4(dl11)(dl1dl2dl11)++2(l1)(dl1d21)(nldl1d21)]f(dl+1,dl+1)+kj=l+1nj(jl)f(dl+1,dj+1)+(kl+1)nk+1f(dl+1,1)+(dl11)[kj=l+1nj(jl+2)f(dl+1,dj+1)+(kl+3)nk+1f(dl+1,1)]+(dl1dl2dl1)[kj=l+1nj(jl+4)f(dl+1,dj+1)+(kl+5)nk+1f(dl+1,1)]++(nldl1d2)[kj=l+1nj(j+l2)f(dl+1,dj+1)+(k+l1)nk+1f(dl+1,1)].

    In particular, we have

    Ak+1=f(1,1)[2(dk2)+4(dk1)(dkdk1dk1)++2k(dkd21)(nk+1dkd21)].

    This completes the proof.

    Corollary 3.2. The degree-weighted Wiener index of a Bethe tree Bk,d is

    DWW(Bk,d)=kl=1Al,

    where

    A1=k1j=2d(d+1)j2(j1)f(d,d+1)+(k1)d(d+1)k2f(d,1),Al=[2(d+12)+4(d+11)((d+1)2(d+1)1)++2(l1)(dl21)(nldl21)]f(d+1,d+1)+k1j=l+1nj(jl)f(d+1,d+1)+(kl)nkf(d+1,1)+(dl11)[k1j=l+1f(d+1,d+1)nj(jl+2)+(kl+2)nkf(d+1,1)]+(dl1dl2dl1)[k1j=l+1nj(jl+4)f(d+1,d+1)+(kl+4)nkf(d+1,1)]++(nldl1d2)[k1j=l+1nj(j+l2)f(d+1,d+1)+(k+l2)nkf(d+1,1)],Ak=f(1,1)[2(d2)+4(d1)(d(d1)1)++2(k1)(dk21)((d1)dk21)].

    Corollary 3.3. The degree-weighted Wiener index of a regular dendrimer tree Tk,d is

    DWW(Tk,d)=k+1l=1Al,

    where

    A1=kj=2nj(j1)f(d,d)+kd(d1)k1f(d,1),Al=[2(d12)+4(d11)((d1)(d2)1)++2(l1)((d1)l21)(nl(d1)l21)]f(d,d)+kj=l+1nj(jl)f(d,d)+(kl+1)nk+1f(d,1)+(d2)[kj=l+1nj(jl+2)f(d,d)+(kl+3)nk+1f(d,1)]+(d1)(d2)[kj=l+1nj(jl+4)f(d,d)+(kl+5)nk+1f(d,1)]++(nl(d1)l2)[kj=l+1nj(j+l2)f(d,d)+(k+l1)nk+1f(d,1)],Ak+1=f(1,1)[2(d12)+4(d11)((d1)(d2)1)++2k((d1)k11)((d1)k1)].

    In this section, the chemical applicability of the SW index is investigated. The acentric factor (AcenFac) is a measure of the non-sphericity of molecules. We consider the correlation between acentric factors of octane isomers and the respective SW indices. The experimental values of acentric factors of octane isomers were taken from http://www.moleculardescriptors.eu/dataset/dataset.htm.

    Using the data from Table 1, we find the correlation of AcenFac with the value of SW index for octane isomers; see Figure 1. The following equations give the regression models for the SW index:

    AcenFac=0.00198×SW+0.008141.
    Table 1.  Experimental values of AcenFac and SW index for octane isomers.
    Molecule AcenFac SW
    Octane 0.397898 202.8093
    2-methyl-heptane 0.377916 191.2453
    3-methyl-heptane 0.371002 182.2057
    4-methyl-heptane 0.371504 179.1925
    3-ethyl-hexane 0.362472 170.5225
    2, 2-dimethyl-hexane 0.339426 170.4970
    2, 3-dimethyl-hexane 0.348247 166.8181
    2, 4-dimethyl-hexane 0.344223 169.9447
    2, 5-dimethyl-hexane 0.35683 179.0977
    3, 3-dimethyl-hexane 0.322596 158.2653
    3, 4-dimethyl-hexane 0.340345 160.7917
    2-methyl-3-ethyl-pentane 0.332433 157.9633
    3-methyl-3-ethyl-pentane 0.306899 149.3210
    2, 2, 3-trimethyl-pentane 0.300816 148.2544
    2, 2, 4-trimethyl-pentane 0.30537 157.5862
    2, 3, 3-trimethyl-pentane 0.293177 145.1517
    2, 3, 4-trimethyl-pentane 0.317422 153.9314
    2, 2, 3, 3-tetramethylbutane 0.255294 135.0271

     | Show Table
    DownLoad: CSV
    Figure 1.  Scatter plot between acentric factor of Octane isomers and their SW index.

    Thus, the SW index can also help to predict the properties of octane isomers.

    In this paper, we propose the SW index, and establish some mathematical relations between the Harary-Sombor index and other classic topological indices. Morover, we obtain the calculation formula of degree-weighted Wiener index for generalized Bethe trees. In addition, some numerical results are discussed. We calculate the SW index of octane isomers. The regression models show that the AcenFac and SW index of octane isomers are highly correlated.

    In 1993, Klein and Randić [12] introduced the notion of resistance distance. Naturally, from the perspective of distance, we similarly propose the degree-weighted resistance-distance index of a graph G and define it as

    DWR(G)={u,v}V(G)f(du,dv)r(u,v),

    where r(u,v) is the resistance distance between u and v. It would be interesting to explore chemical and mathematical properties and possible predictive potential of this index.

    The authors declare they have not used Artificial Intelligence (AI) tools in the creation of this article.

    The authors are thankful to the anonymous referees for their helpful comments that improved the quality of the manuscript. This work was funded by the National Natural Science Foundation of China under Grant No. 12261074.

    The authors declare no conflicts of interest to this work.



    Conflict of interest



    The authors declare no conflict of interest.

    Author contributions



    Conceptualization, A.T., A.M.; methodology, G.M., P.Z., A.T., C.U.M., L.D., D.G., A.M.; writing—original draft preparation, G.M., P.Z., A.T., C.U.M., L.D., D.G., A.M.; writing review and editing, G.M., P.Z., A.T., C.U.M., L.D., D.G., A.M.; visualization, G.M., P.Z., A.T., C.U.M., L.D., D.G., A.M.; supervision, P.Z., A.T., and A.M. All authors have read and agreed to the published version of the manuscript.

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